National Library of Energy BETA

Sample records for macromolecular crystallography mx

  1. SMB, Macromolecular Crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The macromolecular crystallography (MC) program is a major experimental driver for structural biology research, serving the needs of a large number of academic and biotech groups ...

  2. Instrumentation upgrades for the Macromolecular Crystallography beamlines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of the Swiss Light Source | Stanford Synchrotron Radiation Lightsource Instrumentation upgrades for the Macromolecular Crystallography beamlines of the Swiss Light Source Monday, October 29, 2012 - 2:00am SSRL, Bldg. 137, Rm. 322 Martin Fuchs, MX Group, Swiss Light Source; Paul Scherrer Institute (Villigen, Switzerland) A new unified diffractometer - the D3 - has been developed for the three MX beamlines. The first of the instruments is in general user operation at beamline X10SA since April

  3. Introduction to Bayesian methods in macromolecular crystallography...

    Office of Scientific and Technical Information (OSTI)

    Results Journal Article: Introduction to Bayesian methods in macromolecular crystallography Citation Details ... Publication Date: 2011-07-14 OSTI Identifier: 1082292 Report ...

  4. Introduction to Bayesian methods in macromolecular crystallography (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Journal Article: Introduction to Bayesian methods in macromolecular crystallography Citation Details In-Document Search Title: Introduction to Bayesian methods in macromolecular crystallography Authors: Terwilliger, Thomas C [1] + Show Author Affiliations Los Alamos National Laboratory Publication Date: 2011-07-14 OSTI Identifier: 1082292 Report Number(s): LA-UR-11-04079; LA-UR-11-4079 DOE Contract Number: AC52-06NA25396 Resource Type: Journal Article Research Org:

  5. JBlulce Data Acquisition Software for Macromolecular Crystallography

    Energy Science and Technology Software Center (OSTI)

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similarmore » systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest

  6. Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines

    SciTech Connect (OSTI)

    Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz,Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

    2007-07-01

    Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller

  7. Large-volume protein crystal growth for neutron macromolecular crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; Garcia-Ruiz, Juan M.; Hodge, Teresa A.; Huang, Sijay

    2015-03-30

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

  8. Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

    SciTech Connect (OSTI)

    A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

    2011-12-31

    The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

  9. The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; Cohen, Aina E.

    2016-02-24

    The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. As a result, sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.

  10. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

    SciTech Connect (OSTI)

    Tsai, Yingssu; McPhillips, Scott E.; Gonzlez, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

    2013-05-01

    New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

  11. Proposal Submittal and Scheduling Procedures for Macromolecular

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Crystallography | Stanford Synchrotron Radiation Lightsource Proposal Submittal and Scheduling Procedures for Macromolecular Crystallography Beam time for macromolecular crystallography projects is obtained by submitting an SSRL Macromolecular Crystallography Proposal. This proposal is peer reviewed by the Structural Molecular Biology and Biophysics subpanel of the SSRL Proposal Review Panel (PRP) for scientific merit and rating and for criticality of synchrotron radiation use. Proposal

  12. Macromolecular Crystallography - Beamline facilities

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the .forward file and save it. If you have more than one e-mail address or you want other people in your group to receive the notification, add one address per line. Use the...

  13. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

    SciTech Connect (OSTI)

    Stetten, David von; Giraud, Thierry; Carpentier, Philippe; Sever, Franc; Terrien, Maxime; Dobias, Fabien; Juers, Douglas H.; Flot, David; Mueller-Dieckmann, Christoph; Leonard, Gordon A.; Sanctis, Daniele de; Royant, Antoine

    2015-01-01

    The current version of the Cryobench in crystallo optical spectroscopy facility of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed. The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for spectroscopy). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.

  14. Automated macromolecular crystallization screening

    DOE Patents [OSTI]

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  15. Instrumentation upgrades for the Macromolecular Crystallography...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The multi-mode optical spectroscopy module is always online and supports in-situ UVVis absorption, fluorescence and Raman spectroscopy. It is complemented by a complete off-line ...

  16. Goniometer-based Femtosecond Macromolecular Crystallography ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    E. G. Kovaleva, A. C. Kruse, H. T. Lemke, G. Lin, A. Y. Lyubimov, A. Manglik, I. I. Mathews, S. E. McPhillips, S. Nelson, J. W. Peters, N. K. Sauter, C. A. Smith, J. Song, H. P....

  17. Resources for Macromolecular Crystallography | Advanced Photon...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Time GUP Login Proposal Calendar Publications Database CAT Websites: BioCARS GMCA-CAT IMCA-CAT LRL-CAT LS-CAT NE-CAT SBC-CAT SER-CAT Reports and Presentations: Stuctural Bio...

  18. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The atmospheric test films showed why the MX missiles should not be based in the Great ... Military strategists planned to secure the missiles in hardened concrete shelters ...

  19. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational...

  20. Systems Biology in Prokaryote - Eukaryote Symbiosis | Stanford...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Frontier challenges for macromolecular crystallography (MX) now include determining structures of trapped reactive intermediates, large macromolecules and viruses, membrane ...

  1. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE ...

  2. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology ...

  3. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    MX Factor Test films played a strategic-planning role in the debates of the late 1970s and early 1980s about where and how to deploy the MX intercontinental ballistic missile (LGM-118 Peacekeeper). The deployment would have to ensure that the missiles could survive a first strike by an adversary. Military planners were considering placing the missiles in clusters of hardened concrete shelters in the hot, dry Great Basin Desert of Nevada and Utah. Films of atmospheric tests at the Nevada Test

  4. Deformable elastic network refinement for low-resolution macromolecular crystallography

    SciTech Connect (OSTI)

    Schrder, Gunnar F.; Levitt, Michael; Brunger, Axel T.

    2014-09-01

    An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 . Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  5. Method for removing atomic-model bias in macromolecular crystallography

    DOE Patents [OSTI]

    Terwilliger, Thomas C.

    2006-08-01

    Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

  6. Holographic Methods in X-ray Crystallography

    Energy Science and Technology Software Center (OSTI)

    1995-07-28

    The holographic method makes use of partially modeled electron density and experimentally-measured structure factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density, and can incorporate a target electron density, making it similar to solvent flattening. Using both synthetic and experimental data,more » we assess the potential for applying the holographic method to macromolecular x-ray crystallography.« less

  7. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Beamline 8.3.1 Print Tuesday, 20 October 2009 08:55 Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural...

  8. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION...

  9. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    3.1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational...

  10. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural...

  11. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Beamline 8.3.1 Print Tuesday, 20 October 2009 08:55 Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural...

  12. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4.2.2 Print Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL...

  13. Energy optimization of a regular macromolecular crystallography beamline for ultra-high-resolution crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rosenbaum, Gerd; Ginell, Stephan L.; Chen, Julian C.-H.

    2015-01-01

    In this study, a practical method for operating existing undulator synchrotron beamlines at photon energies considerably higher than their standard operating range is described and applied at beamline 19-ID of the Structural Biology Center at the Advanced Photon Source enabling operation at 30 keV. Adjustments to the undulator spectrum were critical to enhance the 30 keV flux while reducing the lower- and higher-energy harmonic contamination. A Pd-coated mirror and Al attenuators acted as effective low- and high-bandpass filters. The resulting flux at 30 keV, although significantly lower than with X-ray optics designed and optimized for this energy, allowed for accuratemore » data collection on crystals of the small protein crambin to 0.38 Å resolution.« less

  14. Cryogenic Neutron Protein Crystallography: routine methods and potential benefits

    SciTech Connect (OSTI)

    Weiss, Kevin L; Tomanicek, Stephen J; NG, Joseph D

    2014-01-01

    The use of cryocooling in neutron diffraction has been hampered by several technical challenges such as the need for specialized equipment and techniques. Recently we have developed and deployed equipment and strategies that allow for routine neutron data collection on cryocooled crystals using off the shelf components. This system has several advantages, compared to a closed displex cooling system such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure we collected a full neutron data set on the BIODIFF instrument on a Toho-1 lactamase structure at 100K.

  15. Microbial Electrochemical Technology (MxCs): Challenges and Opportunities |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Electrochemical Technology (MxCs): Challenges and Opportunities Microbial Electrochemical Technology (MxCs): Challenges and Opportunities Presentation by Jason Ren, University of Colorado Boulder, during the "Technological State of the Art" panel at the Hydrogen, Hydrocarbons, and Bioproduct Precursors from Wastewaters Workshop held March 18-19, 2015. Microbial Electrochemical Technology (MxCs): Challenges and Opportunities (2.69 MB) More Documents &

  16. DOE - NNSA/NFO -- News & Views MX Missle

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    MX Missile, Shelter, Launch Methods Undergo Testing Photo - MX Missle An experimental vertical shelter for the deployment of MX missiles was constructed at the Test Site. If the design had been adopted, the missile would have been placed in an 18-foot diameter, 130-foot-deep vertical silo. At launch the silo would have cut through a 40-foot layer of soil. The missile would then have been fired. Pan Am photo. The Nevada Test Site was selected for several Air Force Peacekeeper (MX) research and

  17. Microbial Electrochemical Technology (MxCs): Challenges and Opportunit...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    More Documents & Publications Microbial Electrolysis Cells (MECs) for High Yield Hydrogen (H2) Production from Biodegradable Materials Microbial Fuel Cell Technologies-MxCs: Can ...

  18. Microbial Fuel Cell Technologies--MxCs: Can They Scale?

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... Technol. 29 30 Conclusions * Microbial Fuel Cell Technologies-- MxCs: Can they scale? Yes 30 MET Companies * Emefcy (Israel) , www.emefcy.com * Cambrian Innovations (Boston, ...

  19. A New Camera for Powder Diffraction of Macromolecular Crystallography at SPring-8

    SciTech Connect (OSTI)

    Miura, Keiko; Inoue, Katsuaki; Goto, Shunji; Ishikawa, Tetsuya; Yamamoto, Masaki; Ueki, Tatzuo

    2004-05-12

    A powder diffractometer of Guinier geometry was developed and tested on a beamline, BL40B2, at SPring-8. The long specimen-to-detector distance, 1,000 mm, is advantageous in recording diffraction from Bragg spacing of 20 nm or larger. The angular resolution, 0.012 degrees, was realized together with the focusing optics, the long specimen-to-detector distance and the small pixel size of Blue-type Imaging Plate detector. Such a high resolution makes the peak separation possible in the powder diffraction from microcrystals with large unit cell and low symmetry of biological macromolecules.

  20. MX Group SpA | Open Energy Information

    Open Energy Info (EERE)

    SpA Place: Villasanta, Italy Zip: 20058 Product: MX group is a turnkey provider of manufacturing plants for PV and other electronic equipment. Coordinates: 45.606895, 9.3066...

  1. Media invited to join students in crystallography experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Media invited to join students in crystallography experiment Media invited to join students in crystallography experiment The student outreach effort is part of the events...

  2. Microcrystallization techniques for serial femtosecond crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    using Photosystem II from Thermosynechococcus elongatus as a model system Microcrystallization techniques for serial femtosecond crystallography using Photosystem II from Thermosynechococcus elongatus as a model system Authors: Kupitz, C., Grotjohann, I., Conrad, C.E., Roy-Chowdhury, S., Fromme, R., and Fromme, P. Title: Microcrystallization techniques for serial femtosecond crystallography using Photosystem II from Thermosynechococcus elongatus as a model system Source: Phil. Trans. R. Soc.

  3. EA-381-A E-T Global (MX).pdf

    Office of Environmental Management (EM)

    79 FreePoint Commodities EA-379 FreePoint Commodities Order authorizing FreePoint Commodities to export electric energy to Mexico. EA-379 Freepoint MX_Revised.docx (155.84 KB) More Documents & Publications EA-380 Freeport Commodities EA-314-A BP Energy Co EA-176 Sempra Energy Trading Corporation

    1 E-T Global Energy EA-381 E-T Global Energy Order authorizing E-T Global Energy to export electric energy to Mexico. EA-381 ET Global MX.docx (155.57 KB) More Documents & Publications EA-381

  4. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Liu, Liu

    2013-10-23

    Serial femtosecond crystallography data on microcrystals of 5-HT2B receptor bound to ergotamine grown in lipidic cubic phase.

  5. AmeriFlux MX-Lpa La Paz

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Oechel, Walter [San Diego State University

    2016-01-01

    This is the AmeriFlux version of the carbon flux data for the site MX-Lpa La Paz. Site Description - As evident by some very large Cardon (5-7 meters), according to Coyle and Roberts, 1975, extent vegetation has likely been around at least 200 years. Until about 15 years ago from 1996, site was used for livestock production and selective firewood extraction. However, when I look over the fence where there has been livestock activity, not much difference

  6. Structural Insight into HIV-1 Restriction by MxB (Journal Article...

    Office of Scientific and Technical Information (OSTI)

    Title: Structural Insight into HIV-1 Restriction by MxB Authors: Fribourgh, Jennifer L. ; Nguyen, Henry C. ; Matreyek, Kenneth A. ; Alvarez, Frances Joan D. ; Summers, Brady J. ; ...

  7. Automated macromolecular crystal detection system and method

    DOE Patents [OSTI]

    Christian, Allen T.; Segelke, Brent; Rupp, Bernard; Toppani, Dominique

    2007-06-05

    An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

  8. Media invited to join students in crystallography experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Media invited to join students in crystallography experiment Media invited to join students in crystallography experiment The student outreach effort is part of the events commemorating 2014 as the International Year of Crystallography. May 16, 2014 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and

  9. Automated High Throughput Drug Target Crystallography

    SciTech Connect (OSTI)

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  10. Lipidic phase membrane protein serial femtosecond crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lipidic phase membrane protein serial femtosecond crystallography Authors: Johansson LC, Arnlund D, White TA, Katona G, Deponte DP, Weierstall U, Doak RB, Shoeman RL, Lomb L, Malmerberg E, Davidsson J, Nass K, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter

  11. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    SciTech Connect (OSTI)

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

  12. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    SciTech Connect (OSTI)

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

  13. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  14. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  15. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  16. Enabling X-ray free electron laser crystallography for challenging...

    Office of Scientific and Technical Information (OSTI)

    Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals Citation Details In-Document Search Title: Enabling X-ray ...

  17. Theoretical crystallography with the Advanced Visualization System

    SciTech Connect (OSTI)

    Younkin, C.R.; Thornton, E.N.; Nicholas, J.B.; Jones, D.R.; Hess, A.C.

    1993-05-01

    Space is an Application Visualization System (AVS) graphics module designed for crystallographic and molecular research. The program can handle molecules, two-dimensional periodic systems, and three-dimensional periodic systems, all referred to in the paper as models. Using several methods, the user can select atoms, groups of atoms, or entire molecules. Selections can be moved, copied, deleted, and merged. An important feature of Space is the crystallography component. The program allows the user to generate the unit cell from the asymmetric unit, manipulate the unit cell, and replicate it in three dimensions. Space includes the Buerger reduction algorithm which determines the asymmetric unit and the space group of highest symmetry of an input unit cell. Space also allows the user to display planes in the lattice based on Miller indices, and to cleave the crystal to expose the surface. The user can display important precalculated volumetric data in Space, such as electron densities and electrostatic surfaces. With a variety of methods, Space can compute the electrostatic potential of any chemical system based on input point charges.

  18. Experimental Station 9-2 | Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Beamline 9-2 is a wiggler beamline dedicated for monochromatic, high-throughput and high-resolution macromolecular crystallography and optimized for SAD and MAD experiments. It can be run in a full remote access mode. It is equipped with a Rayonix MX325 CCD detector and a remote access controlled UV-Vis microspectrophotometer. For aditional information about the experimental capabilities, see http://smb.slac.stanford.edu/index.shtml. Status Open Supported Techniques Macromolecular

  19. MX-2500 thermal processor for the treatment of petroleum refining wastes and contaminated soils

    SciTech Connect (OSTI)

    Swanberg, C. )

    1993-05-01

    Separation and Recovery Systems, Inc. (SRS) of Irvine, California is the market leader in supplying hazardous waste and secondary material dewatering and drying services to the petroleum refining industry. In late 1991, SRS introduced the new generation of dryer technology, the MX-2500. The MX-2500 is an electrically heated dryer system that recovers virtually all of the hydrocarbon value of refinery wastes and secondary materials, while producing a solid residue meeting EPA Land Disposal Restriction (LDR) treatment levels which allows the refinery to land dispose of the solids, thereby realizing two objectives: waste minimization and oil recovery/recycling. 2 figs., 3 tabs.

  20. Fermi surfaces and phase stability of Ba(Fe1 xMx)2As2 (M = Co...

    Office of Scientific and Technical Information (OSTI)

    Fermi surfaces and phase stability of Ba(Fe1 xMx)2As2 (M Co,Ni,Cu,Zn) Citation Details In-Document Search Title: Fermi surfaces and phase stability of Ba(Fe1 xMx)2As2 (M ...

  1. Fermi surfaces and Phase Stability of Ba(Fe1-xMx))2As2 (M=Co...

    Office of Scientific and Technical Information (OSTI)

    Fermi surfaces and Phase Stability of Ba(Fe1-xMx))2As2 (MCo, Ni, Cu, Zn) Citation Details In-Document Search Title: Fermi surfaces and Phase Stability of Ba(Fe1-xMx))2As2 (MCo,...

  2. In meso in situ serial X-ray crystallography of soluble and membrane...

    Office of Scientific and Technical Information (OSTI)

    In meso in situ serial X-ray crystallography of soluble and membrane proteins Citation Details In-Document Search Title: In meso in situ serial X-ray crystallography of soluble and ...

  3. Fermi surfaces and phase stability of Ba(Fe1-xMx)2As2 (M = Co...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Fermi surfaces and phase stability of Ba(Fe1-xMx)2As2 (M Co,Ni,Cu,Zn) ... (EFRC); Center for Defect Physics in Structural Materials (CDP) Sponsoring Org: USDOE ...

  4. Optical properties of MX chain materials: An extended Peierls-Hubbard model

    SciTech Connect (OSTI)

    Bishop, A.R.; Batistic, I.; Gammel, J.T.; Saxena, A.

    1991-01-01

    We describe theoretical modeling of both pure (MX) and mixed-halide (MX{sub x}X{prime}{sub 1-x}) halogen (X)-bridged transition metal (M) linear chain complexes in terms of an extended Peierls-Hubbard, tight-binding Hamiltonian with 3/4-filling of two-bands. Both inter- and intra-site electron-phonon coupling are included. Electronic (optical absorption), lattice dynamic (IR, Raman) and spin (ESR) signatures are obtained for the ground states, localized excited states produced by impurities, doping or photo-excitation -- excitons, polarons, bipolarons, solitons; and the edge states (which occur in mixed-halide crystals, e.g. PtCl{sub x}Br{sub 1-x}). Adiabatic molecular dynamics is used to explore photodecay channels in pure and impure systems for ground states as well as in the presence of pre-existing polaronic states. 12 refs., 3 figs., 1 tab.

  5. Improved ambient-pressure organic superconductor. [Bis(ethylenedithio)TTF-MX/sub 2/

    DOE Patents [OSTI]

    Williams, J.M.; Wang, Hsien-Hau; Beno, M.A.

    1985-05-29

    Disclosed is a new class of organic superconductors having the formula (ET)/sub 2/MX/sub 2/ wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET)/sub 2/AuI/sub 2/ exhibits a transition temperature of 5/sup 0/K which is high for organic superconductors.

  6. Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

    SciTech Connect (OSTI)

    Leimkuhler, B.; Hermans, J.; Skeel, R.D.

    1995-07-01

    A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

  7. Identifying, studying and making good use of macromolecular crystals

    SciTech Connect (OSTI)

    Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

    2014-07-25

    As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.

  8. Size-exclusion chromatography system for macromolecular interaction analysis

    DOE Patents [OSTI]

    Stevens, Fred J.

    1988-01-01

    A low pressure, microcomputer controlled system employing high performance liquid chromatography (HPLC) allows for precise analysis of the interaction of two reversibly associating macromolecules such as proteins. Since a macromolecular complex migrates faster than its components during size-exclusion chromatography, the difference between the elution profile of a mixture of two macromolecules and the summation of the elution profiles of the two components provides a quantifiable indication of the degree of molecular interaction. This delta profile is used to qualitatively reveal the presence or absence of significant interaction or to rank the relative degree of interaction in comparing samples and, in combination with a computer simulation, is further used to quantify the magnitude of the interaction in an arrangement wherein a microcomputer is coupled to analytical instrumentation in a novel manner.

  9. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    SciTech Connect (OSTI)

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  10. Smarter Drugs: How Protein Crystallography Revolutionizes Drug Design

    SciTech Connect (OSTI)

    Smith, Clyde

    2005-04-26

    According to Smith, protein crystallography allows scientists to design drugs in a much more efficient way than the standard methods traditionally used by large drug companies, which can cost close to a billion dollars and take 10 to 15 years. 'A lot of the work can be compressed down,' Smith said. Protein crystallography enables researchers to learn the structure of molecules involved in disease and health. Seeing the loops, folds and placement of atoms in anything from a virus to a healthy cell membrane gives important information about how these things work - and how to encourage, sidestep or stop their functions. Drug design can be much faster when the relationship between structure and function tells you what area of a molecule to target. Smith will use a timeline to illustrate the traditional methods of drug development and the new ways it can be done now. 'It is very exciting work. There have been some failures, but many successes too.' A new drug to combat the flu was developed in a year or so. Smith will tell us how. He will also highlight drugs developed to combat HIV, Tuberculosis, hypertension and Anthrax.

  11. A novel inert crystal delivery medium for serial femtosecond crystallography

    SciTech Connect (OSTI)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

  12. A novel inert crystal delivery medium for serial femtosecond crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; et al

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, themore » structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.« less

  13. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; et al

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals deliveredmore » by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.« less

  14. Macromolecular coal structure as revealed by novel diffusion tests

    SciTech Connect (OSTI)

    Peppas, N.A.; Olivares, J.; Drummond, R.; Lustig, S.

    1990-01-01

    The main goal of the present work was the elucidation of the mechanistic characteristics of dynamic transport of various penetrants (solvents) in thin sections of coals by examining their penetrant uptake, front swelling and stress development. An important objective of this work was the study of coal network structure in different thermodynamically compatible penetrants and the analysis of dynamic swelling in terms of present anomalous transport theories. Interferometry/polariscopy, surface image analysis and related techniques were used to quantify the stresses and solvent concentration profiles in these sections. Dynamic and equilibrium swelling behavior were correlated using the polar interaction contributions of the solvent solubility parameters. The penetrant front position was followed in thin coal sections as a function of time. The initial front velocity was calculated for various coals and penetrants. Our penetrant studies with thin coal section from the same coal sample but with different thickness show that within the range of 150 {mu}m to 1500{mu}m the transport mechanism of dimethyl formamide in the macromolecular coal network is non-Fickian. In fact, for the thickest samples the transport mechanism is predominately Case-II whereas in the thinner samples penetrant uptake may be diffusion-controlled. Studies in various penetrants such as acetone, cyclohexane, methanol, methyl ethyl ketone, toluene and methylene chloride indicated that penetrant transport is a non-Fickian phenomenon. Stresses and cracks were observed for transport of methylene chloride. 73 refs., 88 figs., 15 tabs.

  15. The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Coates, Leighton; Cuneo, Matthew J.; Frost, Matthew J.; He, Junhong; Weiss, Kevin L.; McFeeters, Hana; Tomanicek, Stephen J.; Vandavasi, Venu Gopal; Langan, Paul; Iverson, Erik B.

    2015-07-18

    The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. Moreover, the instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. Finally, the instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

  16. The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

    SciTech Connect (OSTI)

    Coates, Leighton; Cuneo, Matthew J.; Frost, Matthew J.; He, Junhong; Weiss, Kevin L.; McFeeters, Hana; Tomanicek, Stephen J.; Vandavasi, Venu Gopal; Langan, Paul; Iverson, Erik B.

    2015-07-18

    The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. Moreover, the instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. Finally, the instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

  17. Systems Biology in Prokaryote - Eukaryote Symbiosis | Stanford Synchrotron

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Radiation Lightsource Systems Biology in Prokaryote - Eukaryote Symbiosis Monday, June 25, 2012 - 12:00pm SLAC, SSRL Main Conference Room, 137-322 Allen M. Orville, Brookhaven National Laboratory Frontier challenges for macromolecular crystallography (MX) now include determining structures of trapped reactive intermediates, large macromolecules and viruses, membrane proteins, protein-protein complexes, and protein-nucleic acid complexes. Although structure and function are intimately linked,

  18. Workshop: New Advances in Crystallography with Synchrotrons and X-FELs |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Stanford Synchrotron Radiation Lightsource New Advances in Crystallography with Synchrotrons and X-FELs Tuesday, October 25, 2011 - 8:00am 2011 SSRL/LCLS Annual Users Conference This workshop, part of the 2011 SSRL/LCLS Annual Users Conference, will describe resources and results from synchrotron-based micro crystallography and X-FEL-based nanocrystallography, and explore the future of these tools in producing important scientific results

  19. Implications of the focal beam profile in serial femtosecond crystallography

    SciTech Connect (OSTI)

    Galli, Lorenzo; Chapman, Henry N.; Metcalf, Peter

    2015-05-12

    The photon density profile of an X-ray free-electron laser (XFEL) beam at the focal position is a critical parameter for serial femtosecond crystallography (SFX), but is difficult to measure because of the destructive power of the beam. A novel high intensity radiation induced phasing method (HIRIP) has been proposed as a general experimental approach for protein structure determination, but has proved to be sensitive to variations of the X-ray intensity, with uniform incident fluence desired for best performance. Here we show that experimental SFX data collected at the nano-focus chamber of the Coherent X-ray Imaging end-station at the Linac Coherent Light Source using crystals with a limited size distribution suggests an average profile of the X-ray beam that has a large variation of intensity. We propose a new method to improve the quality of high fluence data for HI-RIP, by identifying and removing diffraction patterns from crystals exposed to the low intensity region of the beam. The method requires crystals of average size comparable to the width of the focal spot.

  20. Effective tight-binding model for MX2 under electric and magnetic fields

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Shanavas, Kavungal Veedu; Satpathy, S.

    2015-06-15

    We present a systematic method for developing a five band Hamiltonian for the metal d orbitals that can be used to study the effect of electric and magnetic fields on multilayer MX2 (M=Mo,W and X=S,Se) systems. On a hexagonal lattice of d orbitals, the broken inversion symmetry of the monolayers is incorporated via fictitious s orbitals at the chalcogenide sites. A tight-binding Hamiltonian is constructed and then downfolded to get effective d orbital overlap parameters using quasidegenerate perturbation theory. The steps to incorporate the effects of multiple layers, external electric and magnetic fields are also detailed. We find that anmore » electric field produces a linear-k Rashba splitting around the Γ point, while a magnetic field removes the valley pseudospin degeneracy at the ±K points. Lastly, our model provides a simple tool to understand the recent experiments on electric and magnetic control of valley pseudospin in monolayer dichalcogendies.« less

  1. Measurements of Eh and pH in Compacted MX-80 Bentonite

    SciTech Connect (OSTI)

    Carlsson, Torbjoern; Muurinen, Arto

    2007-07-01

    The low-content free water and high swelling pressure in compacted bentonite, planned to be used as a buffer in nuclear waste repositories, create adverse conditions for direct measurements of the chemical conditions. This paper presents laboratory results from online measurements with Eh and pH electrodes in water-saturated compacted MX-80 bentonite. The Eh was measured with Au and Pt wires as electrodes, while the pH was determined with IrOx electrodes. The latter were prepared in accordance with the method by Yao et al. [1]. The measurements were carried out in two types of cells: 'squeezing cells' and 'diffusion cells'. The squeezing cell excludes almost completely all chemical interactions between the sample and the surrounding environment outside the cell. The diffusion cell, on the other hand, contains a sample that stays in contact with an external solution and therefore allows following of the physico-chemical interaction between the sample and the external solution. The measuring electrodes were positioned inside the cell in the compacted bentonite, while the reference electrode was positioned outside the cell. (authors)

  2. Advanced Protein Characterization Facility | Argonne National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    APCF Argonne's one-stop resource for genomic research, macromolecular crystallography, and synthetic biology More

  3. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; et al

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

  4. Apparatus and method for nanoflow liquid jet and serial femtosecond x-ray protein crystallography

    DOE Patents [OSTI]

    Bogan, Michael J.; Laksmono, Hartawan; Sierra, Raymond G.

    2016-03-01

    Techniques for nanoflow serial femtosecond x-ray protein crystallography include providing a sample fluid by mixing a plurality of a first target of interest with a carrier fluid and injecting the sample fluid into a vacuum chamber at a rate less than about 4 microliters per minute. In some embodiments, the carrier fluid has a viscosity greater than about 3 centipoise.

  5. Effects of Macromolecular Crowding on the Structure of a Protein Complex

    SciTech Connect (OSTI)

    Rajapaksha Mudalige, Ajith Rathnaweera [ORNL; Stanley, Christopher B [ORNL; Todd, Brian [ORNL

    2015-01-01

    Macromolecular crowding can alter the structure and function of biological macromolecules. We used small angle scattering (SAS) to measure the change in size of a protein complex, superoxide dismutase (SOD), induced by macromolecular crowding. Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl- -glucoside ( -MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. SAXS done in the presence of TEG suggests that for further deformation beyond a 9% decrease in volume the resistance to deformation may increase dramatically.

  6. Beyond crystallography: Diffractive imaging using coherent x-ray light sources

    SciTech Connect (OSTI)

    Miao, J.; Ishikawa, T.; Robinson, I. K.; Murnane, M. M.

    2015-04-30

    X-ray crystallography has been central to the development of many fields of science over the past century. It has now matured to a point that as long as good-quality crystals are available, their atomic structure can be routinely determined in three dimensions. However, many samples in physics, chemistry, materials science, nanoscience, geology, and biology are noncrystalline, and thus their three-dimensional structures are not accessible by traditional x-ray crystallography. Overcoming this hurdle has required the development of new coherent imaging methods to harness new coherent x-ray light sources. Here we review the revolutionary advances that are transforming x-ray sources and imaging in the 21st century.

  7. Serial time-resolved crystallography of photosystem II using a femtosecond

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    X-ray laser Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser Authors: Kupitz, Christopher; Basu, Shibom; Grotjohann, Ingo; Fromme, Raimund; Zatsepin, Nadia A.; Rendek, Kimberly N.; Hunter, Mark; Shoeman, Robert L.; White, Thomas A.; Wang, Dingjie; James, Daniel; Yang, Jay-How; Cobb, Danielle E.; Brenda, Reeder; Raymond, G. Sierra; Liu, Haiguang; Barty, Anton; Aquila, Andrew L.; Deponte, Daniel; Kirian, Richard A.; Bari, Sadia; Bergkamp, Jesse J.;

  8. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOE Patents [OSTI]

    Craig, G.D.; Glass, R.; Rupp, B.

    1997-01-28

    A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

  9. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOE Patents [OSTI]

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  10. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

    SciTech Connect (OSTI)

    Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S.

    2004-05-12

    An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.

  11. Combining Electron Crystallography and X-ray Crystallography to Study the MlotiK1 Cyclic Nucleotide-Regulated Potassium Channel

    SciTech Connect (OSTI)

    Clayton, G.; Aller, S; Wang, J; Unger, V; Morais-Cabral, J

    2009-01-01

    We have recently reported the X-ray structure of the cyclic nucleotide-regulated potassium channel, MlotiK1. Here we describe the application of both electron and X-ray crystallography to obtain high quality crystals. We suggest that the combined application of these techniques provides a useful strategy for membrane protein structure determination. We also present negative stain projection and cryo-data projection maps. These maps provide new insights about the properties of the MlotiK1 channel. In particular, a comparison of a 9 {angstrom} cryo-data projection with calculated model maps strongly suggests that there is a very weak interaction between the pore and the S1-S4 domains of this 6 TM tetrameric cation channel and that the S1-S4 domains can adopt multiple orientations relative to the pore.

  12. Accounting for partiality in serial crystallography using ray-tracing principles

    SciTech Connect (OSTI)

    Kroon-Batenburg, Loes M. J. Schreurs, Antoine M. M.; Ravelli, Raimond B. G.; Gros, Piet

    2015-08-25

    Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data. Serial crystallography generates ‘still’ diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a ‘still’ Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R{sub int} factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R{sub int} of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.

  13. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tenboer, Jason; Basu, Shibom; Zatsepin, Nadia; Pande, Kanupriya; Milathianaki, Despina; Frank, Matthias; Hunter, Mark; Boutet, Sebastien; Williams, Garth J.; Koglin, Jason E.; et al

    2014-12-05

    We report that serial femtosecond crystallography using ultrashort pulses from X-ray Free Electron Lasers (XFELs) offers the possibility to study light-triggered dynamics of biomolecules. Using microcrystals of the blue light photoreceptor, photoactive yellow protein, as a model system, we present high resolution, time-resolved difference electron density maps of excellent quality with strong features, which allow the determination of structures of reaction intermediates to 1.6 Å resolution. These results open the way to the study of reversible and non-reversible biological reactions on time scales as short as femtoseconds under conditions which maximize the extent of reaction initiation throughout the crystal.

  14. Damage by X-rays: A Case Study for Metallo-Protein Crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Damage by X-rays: A Case Study for Metallo-Protein Crystallography Junko Yano1,2, Jan Kern3, Klaus-Dieter Irrgang3, Matthew J. Latimer4, Uwe Bergmann4, Pieter Glatzel5, Yulia Pushkar1,2, Jacek Biesiadka6, Bernhard Loll6, Kenneth Sauer1,2, Johannes Messinger7, Athina Zouni3, Vittal K. Yachandra1 1Melvin Calvin Laboratory, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and 2Department of Chemistry, University of California, Berkeley, CA, USA 3Max-Volmer-Laboratorium für

  15. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Jakobi, Arjen J.; Passon, Daniel M.; Knoops, Kevin; Stellato, Francesco; Liang, Mengning; White, Thomas A.; Seine, Thomas; Messerschmidt, Marc; Chapman, Henry N.; Wilmanns, Matthias

    2016-03-01

    The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.

  16. Administered activity and metastatic cure probability during radioimmunotherapy of ovarian cancer in nude mice with {sup 211}At-MX35 F(ab'){sub 2}

    SciTech Connect (OSTI)

    Elgqvist, Joergen . E-mail: jorgen.elgqvist@radfys.gu.se; Andersson, Hakan; Bernhardt, Peter; Baeck, Tom; Claesson, Ingela; Hultborn, Ragnar; Jensen, Holger; Johansson, Bengt R.; Lindegren, Sture; Olsson, Marita; Palm, Stig; Warnhammar, Elisabet; Jacobsson, Lars

    2006-11-15

    Purpose: To elucidate the therapeutic efficacy of {alpha}-radioimmunotherapy of ovarian cancer in mice. This study: (i) estimated the minimum required activity (MRA), giving a reasonable high therapeutic efficacy; and (ii) calculated the specific energy to tumor cell nuclei and the metastatic cure probability (MCP) using various assumptions regarding monoclonal-antibody (mAb) distribution in measured tumors. The study was performed using the {alpha}-particle emitter Astatine-211 ({sup 211}At) labeled to the mAb MX35 F(ab'){sub 2}. Methods and Materials: Animals were inoculated intraperitoneally with {approx}1 x 10{sup 7} cells of the cell line NIH:OVCAR-3. Four weeks later animals were treated with 25, 50, 100, or 200 kBq {sup 211}At-MX35 F(ab'){sub 2} (n = 74). Another group of animals was treated with a nonspecific mAb: 100 kBq {sup 211}At-Rituximab F(ab'){sub 2} (n = 18). Eight weeks after treatment the animals were sacrificed and presence of macro- and microscopic tumors and ascites was determined. An MCP model was developed and compared with the experimentally determined tumor-free fraction (TFF). Results: When treatment was given 4 weeks after cell inoculation, the TFFs were 25%, 22%, 50%, and 61% after treatment with 25, 50, 100, or 200 kBq {sup 211}At-MX35 F(ab'){sub 2}, respectively, the specific energy to irradiated cell nuclei varying between {approx}2 and {approx}400 Gy. Conclusion: As a significant increase in the therapeutic efficacy was observed between the activity levels of 50 and 100 kBq (TFF increase from 22% to 50%), the conclusion was that the MRA is {approx}100 kBq {sup 211}At-MX35 F(ab'){sub 2}. MCP was most consistent with the TFF when assuming a diffusion depth of 30 {mu}m of the mAbs in the tumors.

  17. MxMn8O16 (M = Ag or K) as promising cathode materials for secondary Mg based batteries: The role of the cation M

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Huang, Jianping; Takeuchi, Esther S.; Altug S. Poyraz; Takeuchi, Kenneth J.; Marschilok, Amy C.

    2016-02-15

    Here, AgxMn8O16 (Ag-OMS-2) and KxMn8O16 (K-OMS-2) were investigated as high voltage cathode materials for Mg based batteries. Both MxMn8O16 materials delivered high initial capacities (>180 mA h g–1), and KxMn8O16 showed high cycle stability with a reversible capacity of >170 mA h g–1 after 20 cycles.

  18. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    (7) chains (6) crystallography (6) mathematical solutions (6) solutions (6) Filter by ... Introduction to Bayesian methods in macromolecular crystallography Terwilliger, Thomas C ...

  19. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques -Philippe

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  20. Computer simulation of the CSPAD, ePix10k, and RayonixMX170HS X-ray detectors

    SciTech Connect (OSTI)

    Tina, Adrienne

    2015-08-21

    The invention of free-electron lasers (FELs) has opened a door to an entirely new level of scientific research. The Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory is an X-ray FEL that houses several instruments, each with its own unique X-ray applications. This light source is revolutionary in that while its properties allow for a whole new range of scientific opportunities, it also poses numerous challenges. For example, the intensity of a focused X-ray beam is enough to damage a sample in one mere pulse; however, the pulse speed and extreme brightness of the source together are enough to obtain enough information about that sample, so that no further measurements are necessary. An important device in the radiation detection process, particularly for X-ray imaging, is the detector. The power of the LCLS X-rays has instigated a need for better performing detectors. The research conducted for this project consisted of the study of X-ray detectors to imitate their behaviors in a computer program. The analysis of the Rayonix MX170-HS, CSPAD, and ePix10k in particular helped to understand their properties. This program simulated the interaction of X-ray photons with these detectors to discern the patterns of their responses. A scientist’s selection process of a detector for a specific experiment is simplified from the characterization of the detectors in the program.

  1. Parallel macromolecular delivery and biochemical/electrochemical interface to cells employing nanostructures

    SciTech Connect (OSTI)

    McKnight, Timothy E; Melechko, Anatoli V; Griffin, Guy D; Guillorn, Michael A; Merkulov, Vladimir L; Simpson, Michael L

    2015-03-31

    Systems and methods are described for parallel macromolecular delivery and biochemical/electrochemical interface to whole cells employing carbon nanostructures including nanofibers and nanotubes. A method includes providing a first material on at least a first portion of a first surface of a first tip of a first elongated carbon nanostructure; providing a second material on at least a second portion of a second surface of a second tip of a second elongated carbon nanostructure, the second elongated carbon nanostructure coupled to, and substantially parallel to, the first elongated carbon nanostructure; and penetrating a boundary of a biological sample with at least one member selected from the group consisting of the first tip and the second tip.

  2. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4.2.2 Print Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend Energy range 5,500-16,000eV Monochromator Rosenbaum-Rock Si(111) sagitally focused monochromator Calculated flux (1.9 GeV, 400 mA) 2.5 x 1011 photons/s at 12 keV Resolving power (E/ΔE) 7,000 with Si(111) crystals Endstations Minihutch Detectors

  3. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4.2.2 Print Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend Energy range 5,500-16,000eV Monochromator Rosenbaum-Rock Si(111) sagitally focused monochromator Calculated flux (1.9 GeV, 400 mA) 2.5 x 1011 photons/s at 12 keV Resolving power (E/ΔE) 7,000 with Si(111) crystals Endstations Minihutch Detectors

  4. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4.2.2 Print Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend Energy range 5,500-16,000eV Monochromator Rosenbaum-Rock Si(111) sagitally focused monochromator Calculated flux (1.9 GeV, 400 mA) 2.5 x 1011 photons/s at 12 keV Resolving power (E/ΔE) 7,000 with Si(111) crystals Endstations Minihutch Detectors

  5. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  6. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  7. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  8. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  9. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  10. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  11. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  12. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  13. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  14. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  15. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  16. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Beamline 8.2.2 Print Tuesday, 20 October 2009 08:54 Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size

  17. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  18. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 tesla, single pole) Energy range 5-17 keV (1% max flux) Monochromator Double flat crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 2.5 x 1011 at 11 keV Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0 (h) x 0.35 (v) mrad Endstations Minihutch Detectors 3 x 3

  19. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 tesla, single pole) Energy range 5-17 keV (1% max flux) Monochromator Double flat crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 2.5 x 1011 at 11 keV Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0 (h) x 0.35 (v) mrad Endstations Minihutch Detectors 3 x 3

  20. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4.2.2 Print Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend Energy range 5,500-16,000eV Monochromator Rosenbaum-Rock Si(111) sagitally focused monochromator Calculated flux (1.9 GeV, 400 mA) 2.5 x 1011 photons/s at 12 keV Resolving power (E/ΔE) 7,000 with Si(111) crystals Endstations Minihutch Detectors

  1. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max

  2. Beamline 8.2.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Beamline 8.2.1 Print Tuesday, 20 October 2009 08:53 Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 T, single pole) Energy range 5-16 keV (standard monochromator); 10-13 keV (multilayer) Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec

  3. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size at sample (FWHM) 100 µm Endstations Minihutch

  4. Beamline 8.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Beamline 8.2.2 Print Tuesday, 20 October 2009 08:54 Berkeley Center for Structural Biology (BCSB) Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography (MX) GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend (5.0 T, single pole) Energy range 5-16 keV Monochromator Double crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 3.0 x 1011 photons/sec Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0(h) x 0.5(v) mrad Measured spot size

  5. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 tesla, single pole) Energy range 5-17 keV (1% max flux) Monochromator Double flat crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 2.5 x 1011 at 11 keV Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0 (h) x 0.35 (v) mrad Endstations Minihutch Detectors 3 x 3

  6. Beamline 8.3.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes Source characteristics Superbend magnet (5.0 tesla, single pole) Energy range 5-17 keV (1% max flux) Monochromator Double flat crystal, Si(111) Measured flux (1.9 GeV, 400 mA) 2.5 x 1011 at 11 keV Resolving power (E/ΔE) 7,000 Divergence (max at sample) 3.0 (h) x 0.35 (v) mrad Endstations Minihutch Detectors 3 x 3

  7. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    SciTech Connect (OSTI)

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Miller, R. J. Dwayne

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

  8. A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bunker, Richard D.; Mandal, Kalyaneswar; Bashiri, Ghader; Chaston, Jessica J.; Pentelute, Bradley L.; Lott, J. Shaun; Kent, Stephen B. H.; Baker, Edward N.

    2015-04-07

    Racemic protein crystallography was used to determine the X-ray structure of the predicted Mycobacterium tuberculosis protein Rv1738, which had been completely recalcitrant to crystallization in its natural L-form. Native chemical ligation was used to synthesize both L-protein and D-protein enantiomers of Rv1738. Crystallization of the racemic {D-protein + L-protein} mixture was immediately successful. The resulting crystals diffracted to high resolution and also enabled facile structure determination because of the quantized phases of the data from centrosymmetric crystals. The X-ray structure of Rv1738 revealed striking similarity with bacterial hibernation factors, despite minimal sequence similarity. As a result, we predict that Rv1738,more » which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.« less

  9. Crystallography Without Crystals: Determining the Structure of Individual Biological Molecules and Nanoparticles

    ScienceCinema (OSTI)

    Ourmazd, Abbas [University of Wisconsin, Milwaukee, Wisconsin, USA

    2010-01-08

    Ever shattered a valuable vase into 10 to the 6th power pieces and tried to reassemble it under a light providing a mean photon count of 10 minus 2 per detector pixel with shot noise? If you can do that, you can do single-molecule crystallography. This talk will outline how this can be done in principle. In more technical terms, the talk will describe how the combination of scattering physics and Bayesian algorithms can be used to reconstruct the 3-D diffracted intensity distribution from a collection of individual 2-D diffiraction patterns down to a mean photon count of 10 minus 2 per pixel, the signal level anticipated from the Linac Coherent Light Source, and hence determine the structure of individual macromolecules and nanoparticles.

  10. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; et al

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences ofmore » these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.« less

  11. JBLULCE

    Energy Science and Technology Software Center (OSTI)

    002719MLTPL00 JBlulce Data Acquisition Software for Macromolecular Crystallography http://www.gmca.anl.gov/jbluice-epics/

  12. Browse by Discipline -- E-print Network Subject Pathways: Geosciences...

    Office of Scientific and Technical Information (OSTI)

    Alexander (Alexander Wlodawer) - Macromolecular Crystallography Laboratory, National Cancer Institute Wolf, Martin (Martin Wolf) - Fachbereich Physik, Freie Universitt Berlin ...

  13. Polydimethylsiloxane as a Macromolecular Additive for Enhanced Performance of Molecular Bulk Heterojunction Organic Solar Cells

    SciTech Connect (OSTI)

    Graham, Kenneth R.; Mei, Jianguo; Stalder, Romain; Shim, Jae Won; Cheun, Hyeunseok; Steffy, Fred; So, Franky; Kippelen, Bernard; Reynolds, John R.

    2011-03-15

    The effect of the macromolecular additive, polydimethylsiloxane (PDMS), on the performance of solution processed molecular bulk heterojunction solar cells is investigated, and the addition of PDMS is shown to improve device power conversion efficiency by ~70% and significantly reduce cell-to-cell variation, from a power conversion efficiency of 1.25 0.37% with no PDMS to 2.16 0.09% upon the addition of 0.1 mg/mL PDMS to the casting solution. The cells are based on a thiophene and isoindigo containing oligomer as the electron donor and [6,6]-phenyl-C61 butyric acid methyl ester (PC61BM) as the electron acceptor. PDMS is shown to have a strong influence on film morphology, with a significant decrease in film roughness and feature size observed. The morphology change leads to improved performance parameters, most notably an increase in the short circuit current density from 4.3 to 6.8 mA/cm2 upon addition of 0.1 mg/mL PDMS. The use of PDMS is of particular interest, as this additive appears frequently as a lubricant in plastic syringes commonly used in device fabrication; therefore, PDMS may unintentionally be incorporated into device active layers.

  14. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect (OSTI)

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  15. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

  16. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The deployment would have to ensure that the missiles could survive a first strike by an adversary. Military planners were considering placing the missiles in clusters of hardened ...

  17. DOE F 740-MX

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Form 740M (10-88) MANDATORY DATA COLLECTION AUTHORIZED BY 10 CFR 30, 40, 50, 70, 75, 150, Public Laws 83-703, 93-438, 95-91 OMB Control No. 1910-1800 4. REPORTING PERIOD 3. RIS 2. ATTACHMENT TO a. DOE/NRC 741 a. SHIPPER'S RIS b. RECEIVER'S RIS c. TRANS. NO. d. CORR NO. e. PC f. AC g. DATA CODE b. DOE/NRC 742 c. DOE/NRC 742c 5. TRANSACTION DATA 1. NAME 8a. LINE NO. 9. SIGNATURE (See instructions for provisions regarding confidentiality.) To the best of my knowledge and belief, the information

  18. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

    SciTech Connect (OSTI)

    Pranikar, Jure [Institute Joef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); University of Primorska, (Slovenia); Turk, Duan, E-mail: dusan.turk@ijs.si [Institute Joef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, (Slovenia)

    2014-12-01

    The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.

  19. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    SciTech Connect (OSTI)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties in the surfactant logic distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  20. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; et al

    2016-08-22

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within themore » crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.« less

  1. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patternsmore » with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  2. Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

    SciTech Connect (OSTI)

    Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.; Langan, Paul; Kovalevskyi, Andrey Y.; Heller, William T.

    2015-11-12

    The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg2+ binds first to the M1 site as a complex with ATP and is followed by Mg2+ binding to the M2 site. Furthermore, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.

  3. Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

    SciTech Connect (OSTI)

    Beyerlein, K. R.; Heymann, M.; Kirian, R.; Adriano, L.; Bajt, S.; Knoška, J.; Wilde, F.; Chapman, H. N.

    2015-12-15

    Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.

  4. Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Beyerlein, K. R.; Adriano, L.; Heymann, M.; Kirian, R.; Knoska, J.; Wilde, F.; Chapman, H. N.; Bajt, S.

    2015-12-08

    Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injectionmore » molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquidflow conservation. In conclusion, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.« less

  5. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; et al

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore » to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

  6. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    SciTech Connect (OSTI)

    Cohen, Aina E.; Soltis, S. Michael; Gonzlez, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6- resolution electron density map. With smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of ?2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

  7. Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.; Langan, Paul; Kovalevskyi, Andrey Y.; Heller, William T.

    2015-11-12

    The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg2+ binds first to the M1 site as a complex with ATP and is followed by Mg2+ binding to the M2 site. Furthermore, themore » target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

  8. Measuring and modeling diffuse scattering in protein X-ray crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Fraser, James S.; Wall, Michael E.

    2016-03-28

    X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

  9. Electron impact action spectroscopy of mass/charge selected macromolecular ions: Inner-shell excitation of ubiquitin protein

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rankovic, Milos Lj.; Giuliani, Alexandre; Milosavljevic, Aleksandar R.

    2016-02-11

    In this study, we have performed inner-shell electron impact action spectroscopy of mass and charge selected macromolecular ions. For this purpose, we have coupled a focusing electron gun with a linear quadrupole ion trap mass spectrometer. This experiment represents a proof of principle that an energy-tunable electron beam can be used in combination with radio frequency traps as an activation method in tandem mass spectrometry (MS2) and allows performing action spectroscopy. Electron impact MS2 spectra of multiply protonated ubiquitin protein ion have been recorded at incident electron energies around the carbon 1s excitation. Both MS2 and single ionization energy dependencemore » spectra are compared with literature data obtained using the soft X-ray activation conditions.« less

  10. Systematics of the temperature-dependent interplane resistivity in Ba(Fe1-xMx)₂As₂ (M=Co, Rh, Ni, and Pd)

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tanatar, M. A.; Ni, N.; Thaler, A.; Bud’ko, S. L.; Canfield, P. C.; Prozorov, R.

    2011-07-27

    Temperature-dependent interplane resistivity ρc(T) was measured systematically as a function of transition-metal substitution in the iron-arsenide superconductors Ba(Fe1-xMx)₂As₂, M=Ni, Pd, Rh. The data are compared with the behavior found in Ba(Fe1-xCox)₂As₂, revealing resistive signatures of pseudogap. In all compounds we find resistivity crossover at a characteristic pseudogap temperature T* from nonmetallic to metallic temperature dependence on cooling. Suppression of T* proceeds very similarly in cases of Ni and Pd doping and much faster than in similar cases of Co and Rh doping. In cases of Co and Rh doping an additional minimum in the temperature-dependent ρc emerges for high dopings,more » when superconductivity is completely suppressed. These features are consistent with the existence of a charge gap covering part of the Fermi surface. The part of the Fermi surface affected by this gap is notably larger for Ni- and Pd-doped compositions than in Co- and Rh-doped compounds.« less

  11. A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography

    SciTech Connect (OSTI)

    Bunker, Richard D.; Mandal, Kalyaneswar; Bashiri, Ghader; Chaston, Jessica J.; Pentelute, Bradley L.; Lott, J. Shaun; Kent, Stephen B. H.; Baker, Edward N.

    2015-04-07

    Racemic protein crystallography was used to determine the X-ray structure of the predicted Mycobacterium tuberculosis protein Rv1738, which had been completely recalcitrant to crystallization in its natural L-form. Native chemical ligation was used to synthesize both L-protein and D-protein enantiomers of Rv1738. Crystallization of the racemic {D-protein + L-protein} mixture was immediately successful. The resulting crystals diffracted to high resolution and also enabled facile structure determination because of the quantized phases of the data from centrosymmetric crystals. The X-ray structure of Rv1738 revealed striking similarity with bacterial hibernation factors, despite minimal sequence similarity. As a result, we predict that Rv1738, which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.

  12. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen -Hsiang; Parks, Jerry M.; Smith, Jeremy C.; Weiss, Kevin L.; Keen, David A.; Blakeley, Matthew P.; Louis, John M.; et al

    2016-03-09

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

  13. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    SciTech Connect (OSTI)

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

  14. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

  15. Poly(ethylene oxide)-Assisted Macromolecular Self-Assembly of Lignin in ABS Matrix for Sustainable Composite Applications

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Akato, Kokouvi M.; Tran, Chau D.; Chen, Jihua; Naskar, Amit K.

    2015-11-05

    Here we report the compatibilization of biomass-derived lignin polymer in acrylonitrile butadiene styrene (ABS) thermoplastic matrix without loss of mechanical properties via poly(ethylene oxide) (PEO)-mediated macromolecular self-assembly. ABS was blended with lignin in different concentrations, and blends with 10 wt % PEO (relative to lignin) were prepared. The relative tensile strength improved slightly at low lignin content but diminished rapidly as the lignin content was increased. However, the inclusion of PEO as an interfacial adhesion promoter helped avoid deleterious effects. Dynamic mechanical analysis showed that PEO plasticized the hard phase and thus lowered the activation energy (Ea) for its relaxationmore » but caused stiffening of the soft phase and increased its Ea. Microscopy revealed that incorporating lignin in ABS led to the statistical dispersion of discrete lignin domains (300–1000 nm) which, after PEO addition, were reduced to smaller interconnected particles (200–500 nm). The lignin-extended partially renewable ABS resins showed shear-thinning behavior and reduced viscosity compared to neat ABS. The preferred lignin-loaded compositions reinforced with 20 vol % chopped carbon fibers exhibited mechanical performances (77–80 MPa) equivalent to those of reinforced ABS materials reportedly used in 3D printing applications. In conclusion, this approach could lower the cost of ABS while reducing its carbon footprint.« less

  16. Poly(ethylene oxide)-Assisted Macromolecular Self-Assembly of Lignin in ABS Matrix for Sustainable Composite Applications

    SciTech Connect (OSTI)

    Akato, Kokouvi M.; Tran, Chau D.; Chen, Jihua; Naskar, Amit K.

    2015-11-05

    Here we report the compatibilization of biomass-derived lignin polymer in acrylonitrile butadiene styrene (ABS) thermoplastic matrix without loss of mechanical properties via poly(ethylene oxide) (PEO)-mediated macromolecular self-assembly. ABS was blended with lignin in different concentrations, and blends with 10 wt % PEO (relative to lignin) were prepared. The relative tensile strength improved slightly at low lignin content but diminished rapidly as the lignin content was increased. However, the inclusion of PEO as an interfacial adhesion promoter helped avoid deleterious effects. Dynamic mechanical analysis showed that PEO plasticized the hard phase and thus lowered the activation energy (Ea) for its relaxation but caused stiffening of the soft phase and increased its Ea. Microscopy revealed that incorporating lignin in ABS led to the statistical dispersion of discrete lignin domains (300–1000 nm) which, after PEO addition, were reduced to smaller interconnected particles (200–500 nm). The lignin-extended partially renewable ABS resins showed shear-thinning behavior and reduced viscosity compared to neat ABS. The preferred lignin-loaded compositions reinforced with 20 vol % chopped carbon fibers exhibited mechanical performances (77–80 MPa) equivalent to those of reinforced ABS materials reportedly used in 3D printing applications. In conclusion, this approach could lower the cost of ABS while reducing its carbon footprint.

  17. Bent Diamond Crystals and Multilayer Based Optics at the new 5-Station Protein Crystallography Beamline 'Cassiopeia' at MAX-lab

    SciTech Connect (OSTI)

    Mammen, Christian B.; Als-Nielsen, Jens; Ursby, Thomas; Thunnissen, Marjolein

    2004-05-12

    A new 5-station beamline for protein crystallography is being commissioned at the Swedish synchrotron light source MAX-II at Lund University. Of the 2K/{gamma} = 14 mrad horizontal wiggler fan, the central 2 mrad are used and split in three parts. The central 1 mrad will be used for a station optimized for MAD experiments and on each side of the central fan, from 0.5 mrad to 1 mrad, there are two fixed energy stations using different energies of the same part of the beam. These, in total five stations, can be used simultaneously and independently for diffraction data collection. The two upstream monochromators for the side stations are meridionally bent asymmetric diamond(111) crystals in Laue transmission geometry. The monochromators for the downstream side stations are bent Ge(111) crystals in asymmetric Bragg reflection geometry. Curved multilayer mirrors inserted in the monochromatic beams provide focusing in the vertical plane. The first side station is under commissioning, and a preliminary test protein data set has been collected.

  18. Single-Crystal Raman Spectroscopy and X-ray Crystallography at Beamline X26-C of the NSLS

    SciTech Connect (OSTI)

    D Stoner-Ma; J Skinner; D Schneider; M Cowan; R Sweet; A Orville

    2011-12-31

    Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of 'mystery density', i.e. ambiguous or unknown features within the electron density maps, especially at {approx}2 {angstrom} resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data.

  19. Women @ Energy: Jasmine Hasi | Department of Energy

    Office of Environmental Management (EM)

    radiation sensors for high energy physics and macromolecular crystallography applications. Dr. Jasmine Hasi is an expert in designing and fabricating silicon radiation ...

  20. SSRL30

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    users. Meeting sessions will focus on interdisciplinary applications of small angle X-ray scattering, macromolecular crystallography, microspectroscopy and diffraction, and...

  1. Data Collection & Analysis Software | Stanford Synchrotron Radiation...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Collection & Analysis Software Techniques Data Collection Packages Data Analysis Packages Macromolecular Crystallography See http:smb.slac.stanford.edufacilities See http:...

  2. MitoNEET

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Macromolecular Crystallography at SSRL UCSD Press Release 2 November 2007 Potential Diabetes Drug Target summary written by Amber Dance, SLAC Communication Office Scientists...

  3. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2007-10-02

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  4. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  5. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

    SciTech Connect (OSTI)

    Dror, Oranit Lasker, Keren; Nussinov, Ruth; Wolfson, Haim

    2007-01-01

    A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented. Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6–10 Å resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 Å resolution.

  6. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    SciTech Connect (OSTI)

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  7. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

  8. LANSCE | Lujan Center | Instruments | PCS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Crystallography Station | PCS Structural Enzymology The Protein Crystallography Station (PCS) at LANSCE is a high performance beam line that is funded by DOE-OBER. It forms the core of a capability for joint neutron and X-ray macromolecular structure and function determination. The PCS is the first protein crystallography beam line to be built at a spallation neutron source in North America and is one of the world's premier neutron crystallography instruments. The beam-line exploits the

  9. EA-336_ConocoPhillips_MX.pdf

    Office of Environmental Management (EM)

  10. EA-338_Shell_Energy_MX.pdf

    Office of Environmental Management (EM)

  11. EA-341_Photovoltaic_MX.pdf

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  12. EA-346_Credit_Suisse_MX.pdf

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  13. EA-373_EDF_MX.pdf

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  14. EA-378 CPM MX.pdf

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  15. EA-383 Pilot Power MX.pdf

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  16. EA-383 Pilot Power MX_0.pdf

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  17. EA-384 NRGPML MX.pdf

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  18. EA-386 GSEMNA - MX.pdf

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  19. EA-387 Energia Renovable (MX).pdf

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  20. EA-401 Lonestar (MX).pdf

    Office of Environmental Management (EM)

  1. EA-401 Lonestar (MX)_0.pdf

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  2. EA-402 ESJUS MX.pdf

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  3. EA-403 Frontera Marketing (MX).pdf

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  4. EA-403 Frontera Marketing (MX).pdf

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  5. EA-406 Sempra Generation (MX).pdf

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  6. EA-413 Elan Energy MX.pdf

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  7. EA-417 Tenaska Energia (MX).pdf

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  8. EA-418 Termoelectrica US (MX).pdf

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  9. EA-184-B MSCG MX.pdf

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  10. EA-206-B Frontera (MX).pdf

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  11. EA-247-A_Constellation_MX.pdf

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  12. EA-289-B Intercom MX.pdf

    Office of Environmental Management (EM)

    Intercom Energy, Inc EA-289 Intercom Energy, Inc Order authorizing Intercom Energy, Inc to export electric energy to Mexico EA-289 Intercom Energy, Inc (1.04 MB) More Documents & Publications EA-289-A Intercom Energy, Inc EA-289-A Intercom Energy, Inc.

    -A Intercom Energy, Inc EA-289-A Intercom Energy, Inc Order authorizing Intercom Energy, Inc to export electric energy to Mexico EA-289-A Intercom Energy, Inc (1.18 MB) More Documents & Publications EA-289-A Intercom Energy, Inc.

  13. Neutron crystallography aids drug design

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Los Alamos and currently at Oak Ridge National Laboratory, and Robert McKenna, David Silverman and Mayank Aggarwal of the University of Florida. The U.S. Department of Energy...

  14. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    who shared the 1988 Nobel Prize in Chemistry for his research using X-ray ... Johann Deisenhofer, Ph.D. The 1988 Nobel Prize in Chemistry Goes to Johann Deisenhofer ...

  15. Powder Diffraction Crystallography Instructional Materials

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to Least-squares Fitting: A mostly descriptive approach A non-rigorous introduction to linear algebra, linear and non-linear least squares and related concepts. Software...

  16. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    Johann Deisenhofer Courtesy of UT Southwestern Medical Center "Johann Deisenhofer, Ph.D. is a Professor at UT Southwestern who shared the 1988 Nobel Prize in Chemistry for...

  17. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    in Biomolecular Science."1 Deisenhofer collaborated with DOE scientists on structural biology studies at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory ...

  18. Crystal structure of N-{N-[N-acetyl-(S)-leucyl]-(S)-leucyl}norleucinal...

    Office of Scientific and Technical Information (OSTI)

    ... Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press. Paul, S. (2008). BioEssays, ...

  19. Experimental Run Schedules for Previous Years | Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Run Schedules for Previous Years SPEAR Operating Maintenance Beam Line Schedule Accelerator Physics FY2015 X-ray VUV, BL13 Macromolecular Crystallography FY2014 X-ray VUV, BL13...

  20. Beamline 4.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Beamline 4.2.2 Beamline 4.2.2 Print Tuesday, 20 October 2009 08:31 Molecular Biology Consortium Multiple-Wavelength Anomalous Diffraction (MAD) and Macromolecular Crystallography...

  1. --No Title--

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Radiation Sources (CARS) 434-D Sector 16 HP-CAT High Pressure CAT 434-E Sector 17 IMCA-CAT Industrial Macromolecular Crystallography Association 435-A Sector 18 Bio-CAT...

  2. Experimental Station 7-1 | Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Beamline 7-1 is a wiggler side-station beamline dedicated for monochromatic, high-throughput, high-resolution macromolecular crystallography. It is SAD and MAD capable and can be run in a full remote access mode. It is equipped with an ADSC Q315R CCD detector. For aditional information about the experimental capabilities, see http://smb.slac.stanford.edu/index.shtml. Status Open Supported Techniques Macromolecular Crystallography Multi wavelength anomalous diffraction (MAD) Single wavelength

  3. A national facility for biological cryo-electron microscopy

    SciTech Connect (OSTI)

    Saibil, Helen R.; Grnewald, Kay; Stuart, David I.

    2015-01-01

    This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron. Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

  4. Improving the accuracy of macromolecular structure refinement

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 resolution, starting from different initial models...

  5. Prospects for Simulating Macromolecular Surfactant Chemistry...

    Office of Scientific and Technical Information (OSTI)

    at the Ocean-Atmosphere Boundary Biogenic lipids and polymers are surveyed for their ... Lipids and denatured protein-like polymers dominate at the selected locations. The ...

  6. Proposal Submittal and Scheduling Procedures for Macromolecular...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    This proposal is peer reviewed by the Structural Molecular Biology and Biophysics subpanel ... Once a complete proposal is received, it is sent to the Structural Molecular Biology and ...

  7. Continuous mutual improvement of macromolecular structure models...

    Office of Scientific and Technical Information (OSTI)

    ... Country of Publication: United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION structure determination; model quality; data ...

  8. Center for Nanophase Materials Sciences (CNMS) - Macromolecular...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Polymerization: Extensive expertise in free radical and controlled radical (ATRP, NMP, RAFT) polymerizations. Ring Opening Polymerization: Expertise in the controlled ring-opening...

  9. Nanostructure, Chemistry and Crystallography of Iron Nitride...

    Broader source: Energy.gov (indexed) [DOE]

    1 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer Evaluation lm043allard2011p.pdf (1.26 MB) More Documents & Publications ...

  10. Warm Dense Crystallography: Digging Deeper into WDM

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Department of Energy Want a Tax Credit for a Small Wind System? Be Sure It's Certified! Want a Tax Credit for a Small Wind System? Be Sure It's Certified! August 3, 2015 - 3:54pm Addthis A small wind turbine can produce enough energy to cover the electricity costs of the average American home. | Photo from Bergey Windpower Co., Inc.; NREL 13830 A small wind turbine can produce enough energy to cover the electricity costs of the average American home. | Photo from Bergey Windpower Co., Inc.;

  11. MxEnergy Electric, Inc. (Connecticut) | Open Energy Information

    Open Energy Info (EERE)

    1-877-997-9995 Website: www.constellation.compagesmx Twitter: @constellationeg Facebook: https:www.facebook.comConstellationEnergy Outage Hotline: 1-877-997-9995...

  12. EA-279_UNS__MX.pdf | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    9UNSMX.pdf EA-279UNSMX.pdf EA-279 PDF icon EA-279UNSMX.pdf More Documents & Publications CX-004879: Categorical Exclusion Determination ANTELOPE VALLEY SOLAR RANCH ...

  13. PP-304_GDD_-_WAPA__San_Luis_MX.pdf

    Office of Environmental Management (EM)

  14. Microbial Electrochemical Technology (MxCs): Challenges and Opportunit...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    and Opportunities e - e - V - + Desalination Electricity H 2 CH 4 H 2 O 2 organics ... - mainly organic chemicals Microbial Desalination Cell (MDC) Desalinated water, in ...

  15. EA-294-B TexMex MX.pdf

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  16. EA-318-A_AEPEP_Inc__MX.pdf

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  18. EA-331-A_RBS_Rescission_MX.pdf

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  19. EA-331_Royal_Bank_of_Scotland_MX.pdf

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  20. EA-336-A ConocoPhillips (MX).pdf

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  1. EA-338-A Shell Energy (MX).pdf

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  2. EA-357-A Hunt Electric Power (MX).pdf

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  3. EA-363-A Noble Americas MX.pdf

    Office of Environmental Management (EM)

    3 Noble Americas Gas & Power Corporation EA-363 Noble Americas Gas & Power Corporation Order authorizong Noble Americas Gas & Power Corporation to export electric energy to Mexico EA-363 Noble Americas Gas & Power Corporation (2.58 MB) More Documents & Publications Record of Categorical Exclusion (CS) Determination, Office of Electricity Delivery and Energy Reliability (OE): EA-363 Noble Americas Gas & Power Corporation EA-364 Noble Americas Gas & Power Corporation

  4. EA-375-A Rainbow Energy (MX).pdf

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  5. EA-378-A Cargill Power Mkts (MX).pdf

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  6. EA-405 Del Norte Energy (MX).pdf

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  7. EA-413 Elan Energy Svcs. (MX).pdf

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  8. EA-415 Lion Shield Energy (MX).pdf

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  9. EA-415 Lion Shield Energy (MX)_0.pdf

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  10. EA-48-I El Paso (MX).pdf

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  11. Microbial Fuel Cell Technologies—MxCs: Can They Scale?

    Broader source: Energy.gov [DOE]

    Presentation by Bruce Logan, Penn State University, during the "Technological State of the Art" panel at the Hydrogen, Hydrocarbons, and Bioproduct Precursors from Wastewaters Workshop held March 18–19, 2015.

  12. MxEnergy Electric, Inc. (Pennsylvania) | Open Energy Information

    Open Energy Info (EERE)

    861 Data Utility Id 50149 This article is a stub. You can help OpenEI by expanding it. Utility Rate Schedules Grid-background.png Average Rates Residential: 0.0819kWh...

  13. EA-106 Arizona Public Service (MX).pdf

    Office of Environmental Management (EM)

    EA-1037; Final Environmental Assessment for the Uranium Lease Management Program July 1995 (DOE/EA-1037) Table of Contents Glossary 1.0 Introduction 2.0 Purpose and Need for Action 3.0 Description of Alternatives 4.0 Affected Environment 5.0 Environmental Impacts 6.0 List of Persons Consulted 7.0 References Figures Figure 1. Uranium Lease Management Program Lease Tract Map Figure 2. Transportation Haul Routes Figure 3. Uravan Lease Tract Area Figure 4. Paradox Valley Lease Tract Area Figure 5.

  14. EA-149 PacifiCorp (MX).pdf

    Office of Environmental Management (EM)

  15. EA-184-A_Morgan_Stanley_MX.pdf

    Office of Environmental Management (EM)

    4: Record Hill Wind Project in Roxbury, ME EA-1824: Record Hill Wind Project in Roxbury, ME July 1, 2011 EA-1824: Final Environmental Assessment Loan Guarantee to Record Hill Wind, LLC for Construction of a Wind Energy Project in Roxbury, Maine July 11, 2011 EA-1824: Finding of No Significant Impact Loan Guarantee to Record Hill Wind, LLC, for the Record Hill Wind Project, Maine Department of Energy

    6: AV Solar Ranch One Project in Los Angeles and Kern Counties, CA EA-1826: AV Solar Ranch

  16. EA-247-D Constellation NewEnergy (MX).pdf

    Office of Environmental Management (EM)

  17. EA-289-C Intercom Energy MX.pdf

    Office of Environmental Management (EM)

  18. MxEnergy Electric, Inc. (Massachusetts) | Open Energy Information

    Open Energy Info (EERE)

    Place: Massachusetts Phone Number: 1-866-237-7693 Website: www.constellation.compagesmx Twitter: @ConstellationEG Facebook: https:mbasic.facebook.comConstellationEnergy Outage...

  19. Schoenborn wins Bau Neutron Award

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Schoenborn wins Bau Neutron Award Schoenborn wins Bau Neutron Award The American Crystallographic Association (ACA) has selected retired Laboratory Senior Fellow Benno Schoenborn to receive the 2016 Bau Neutron Diffraction Award. August 12, 2015 Benno Schoenborn Benno Schoenborn Communications Office (505) 667-7000 Schoenborn is honored for his pioneering research in macromolecular neutron crystallography and the design and development of the neutron crystallography beamline (Protein

  20. SSRL HEADLINES Nov 2002

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    5 November, 2002 __________________________________________________________________________ Contents of This Issue: Science Highlight - Towards the Chemically Specific Structure of Amorphous Materials: Anomalous X-ray Scattering from a Molybdenum-Germanium Alloy U.S. Secretary of Energy Spencer Abraham Visits SLAC Critical Decision 1 Approval Moves LCLS Project Forward SLAC-DESY MOU Amped Up and Ready to Go! Organizational Changes in Macromolecular Crystallography Group User Research

  1. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    SciTech Connect (OSTI)

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.

  2. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure ofmore » sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.« less

  3. Towards time-resolved serial crystallography in a microfluidic...

    Office of Scientific and Technical Information (OSTI)

    Authors: Pawate, Ashtamurthy S. ; Srajer, Vukica ; Schieferstein, Jeremy ; Guha, Sudipto ; Henning, Robert ; Kosheleva, Irina ; Schmidt, Marius ; Ren, Zhong ; Kenis, Paul J.A. ; ...

  4. Workshop: New Advances in Crystallography with Synchrotrons and...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    with Synchrotrons and X-FELs Tuesday, October 25, 2011 - 8:00am 2011 SSRLLCLS Annual Users Conference This workshop, part of the 2011 SSRLLCLS Annual Users...

  5. Serial snapshot crystallography for materials science with SwissFEL

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dejoie, Catherine; Smeets, Stef; Baerlocher, Christian; Tamura, Nobumichi; Pattison, Philip; Abela, Rafael; McCusker, Lynne B.

    2015-04-21

    New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of datamore » can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.« less

  6. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Onartuzumab (pink) binds to MET (green and blue) on the surface of a cell that's preventing the binding of HGF (red). Image credit: David Wolf, Viscira, LLC. MET is activated by ...

  7. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Geek-Up[10.29.2010]: The Halloween Special Geek-Up[10.29.2010]: The Halloween Special October 29, 2010 - 5:22pm Addthis Niketa Kumar Niketa Kumar Public Affairs Specialist, Office of Public Affairs The Geek-Up[date] team is pretty stoked about Halloween this year. In fact, it's probably one of our favorite holidays. While the menacing and magical alike dedicate October to all things mischievous, the rest of the year they are some of the most energy-conscious, money-saving monsters around. For

  8. Time-resolved serial crystallography captures high-resolution...

    Office of Scientific and Technical Information (OSTI)

    ; Srajer, Vukica ; Henning, Robert ; Schwander, Peter ; Fromme, Raimund ; Ourmazd, Abbas ; Moffat, Keith ; Van Thor, Jasper J. ; Spence, John C.H. ; Fromme, Petra ; Chapman,...

  9. Identification of phases, symmetries and defects through local crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Belianinov, Alex; He, Qian; Kravchenko, Mikhail; Jesse, Stephen; Borisevich, Albina; Kalinin, Sergei V.

    2015-07-20

    Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clusteringmore » and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.« less

  10. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    I. ; McPhillips, Scott E. ; Nelson, Silke ; Peters, John W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; Uervirojnangkoorn, ...

  11. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    Brian K. ; Kovaleva, Elena G. ; Kruse, Andrew C. ; Lemke, ... W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; ...

  12. Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic

    Broader source: Energy.gov (indexed) [DOE]

    U.S. Department of Energy Office of Inspector General Office of Audit Services Audit Report Nanoscale Materials Safety at the Department's Laboratories DOE/IG-0788 February 2008 Department of Energy Washington, DC 2 0 5 8 5 February 28, 2008 MEMORANDUM FOR FROM: Inspector General SUBJECT: IhTFORMATION: Audit Report on "Nanoscale Materials Safety at the Department's Laboratories" BACKGROUND The National Nanotechnology Initiative was established as a multi-agency research and

  13. Serial femtosecond crystallography of soluble proteins in lipidic...

    Office of Scientific and Technical Information (OSTI)

    of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP...

  14. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    I. ; McPhillips, Scott E. ; Nelson, Silke ; Peters, John W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; Uervirojnangkoorn,...

  15. Identification of phases, symmetries and defects through local crystallography

    SciTech Connect (OSTI)

    Belianinov, Alex; He, Qian; Kravchenko, Mikhail; Jesse, Stephen; Borisevich, Albina; Kalinin, Sergei V.

    2015-07-20

    Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clustering and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.

  16. Serial femtosecond crystallography of soluble proteins in lipidic...

    Office of Scientific and Technical Information (OSTI)

    structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting...

  17. On the protonation states, hydrogen bonding and catalytic mechanism of family 11 glycosidases: Direct visualization with neutrons

    SciTech Connect (OSTI)

    Fisher, Suzanne Zoe; Graham, David E.; Hanson, Leif; Kovalevskyi, Andrii Y.; Langan, Paul; Parks, Jerry M.; Wan, Qun; Ostermann, Andreas; Schrader, Tobias

    2015-10-06

    Most enzymatic reactions involve hydrogen or proton transfer among the enzyme, substrate, and water at physiological pH. Thus, enzyme catalysis cannot be fully understood without accurate mapping of hydrogen atom positions in these macromolecular catalysts. Direct information on the location of hydrogen atoms can be obtained using neutron crystallography. We used neutron crystallography and biomolecular simulation to characterize the initial stage of the glycoside hydrolysis reaction catalyzed by a family 11 glycoside hydrolase. We provide evidence that the catalytic glutamate residue alternates between two conformations bearing different basicities, first to obtain a proton from the bulk solvent, and then to deliver it to the glycosidic oxygen to initiate the hydrolysis reaction.

  18. Ringleader: Jay Nix, Beamline Director for the Molecular Biology Consortium

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Jay Nix, Beamline Director for the Molecular Biology Consortium Print Jay Nix started started the user program at Beamline 4.2.2 back in 2004, shortly after the Molecular Biology Consortium built the beamline. The macromolecular crystallography beamline is a little different than most at the ALS because it's privately managed by a consortium of 10 Midwest universities that pooled their money together to build the beamline, and now continue to do so to maintain it. Nix serves about 50 labs,

  19. Proposal Submittal and Scheduling Procedures for Research | Stanford

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Synchrotron Radiation Lightsource Proposal Submittal and Scheduling Procedures for Research New Proposals Standard GU Proposals Instructions for New Standard Proposals (Not LOI or Rapid Access) Tips for How to Wow Rapid Access Letter of Intent (LOI) Proposal Extension Requests X-ray/VUV Macromolecular Crystallography Beam Time Allocation/Scheduling How to Request Beam Time SSRL Access Policy SSRL Schedules Publications & Reports New Proposals SSRL operates as a dedicated synchrotron

  20. SSRL Science | Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science SSRL Science Visit our Science Highlights Archive and list of User and Staff Publications for examples of SSRL user research. Accelerator Physics Macromolecular Crystallography (SMB) Magnetic Dichroism Spectroscopy & Microscopy Materials Scattering Molecular Environmental & Interface Science Near Edge X-ray Absorption Fine Structure (NEXAFS) SAXS Materials Science Powder Diffraction Small Angle Scattering/Diffraction (SMB) Total X-ray Reflection Fluorescence (TXRF) X-ray

  1. Microsoft Word - RNA_polymerase_Kornberg_04.doc

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Inner Workings of RNA Polymerase: How Genetic Information is Transcribed The research group of Professor Roger Kornberg of Stanford University has studied RNA polymerase II for more than 20 years. In 2000, his group solved the atomic-level structure of RNA polymerase, a macromolecular machine that transcribes genetic information, using crystallography diffraction data collected at SSRL [1]. The structure was featured on the cover of Science Magazine in the April 28, 2000 issue (Fig. 1). One

  2. Forms & Applications | Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Forms & Applications Forms: Before You Arrive User Information Log in to the User Portal to Register or Update Contact Informatioin Proposals Submit Proposals via User Portal (including Rapid Access and Letters of Intent) Proposal Extension Requests X-ray/VUV/SMB Macromolecular Crystallography (MC) User Agreements Non-Proprietary User Agreement Proprietary Research User Agreement Beam Time & Support Requests Log in to User Portal to Submit Beam Time or User Support Requests Computer

  3. SSRL HEADLINES April 2005

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    0 April, 2005 __________________________________________________________________________ Contents of this Issue: Science Highlight - First SPPS Results: Electro-optic Sampling and Ultra-fast Melting Science Highlight - Chemically Treated Wood Less Toxic than Feared SSRL/SLAC Hosts International FEL Conference, August 21-26, 2005 The 2005 SMB Summer School September 12-15, 2005 SSRL Users Visit Washington, DC New Developments in Macromolecular Crystallography Protein Model Building Research

  4. SSRL HEADLINES June 2011

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 June, 2011 __________________________________________________________________________ Contents of this Issue: From the Director of SSRL: Looking Ahead Science Highlight - Estimating Cr(VI) in Coal-Derived Fly-Ash Science Highlight - Staying One Step Ahead of Antibiotic Resistance Science Highlight - SSRL's Microfocus Macromolecular Crystallography Beam Line 12-2 First SSRL Pump-Probe Experiments Under Way SSRL X-rays Reveal Patterns in the Plumage of the First Birds Upcoming SSRL Events:

  5. Science Summary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Kohen Research UI News Release SSRL Macromolecular Crystallography » Share this Article Laboratree Ologeez SciLink LabSpaces Novel Mechanism for DNA Biosynthesis in Organisms with Gene thyX could Lead to Better Antibiotics summary written by Raven Hanna Before DNA is made, the subunits composing DNA must be made. The essential process of making one of these subunits, thymidine monophosphate (TMP), was thought to be similar for most living things, but scientists recently discovered that some

  6. Science Summary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    03, 2008 » Links Scientific Highlight Tainer Website Scripps Press Release » Share this Article Laboratree Ologeez SciLink LabSpaces Role of Specific Protein Mutations in Causing Human Disease Revealed summary written by Brad Plummer, SLAC Communication Office Scientists are one step closer to understanding a piece of the machinery involved in DNA transcription and repair, thanks to work done in part at the SSRL macromolecular crystallography Beam Line 11-1. The team, led by The Scripps

  7. Microsoft Word - TCP1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    March 2016 Structure, Inhibition and Regulation of Two-pore Channel TPC1 from Arabidopsis thaliana Using macromolecular crystallography beam lines at SSRL and the ALS scientists Alexander F. Kintzer and Robert M. Stroud at the University of California, San Francisco (UCSF) determined the structure of the first intracellular, voltage-gated, transmembrane protein ion channel, called two-pore channel 1 or TPC1, with an allosteric inhibitor Ned-19 bound to the outside of the channel. Their structure

  8. Profile for Thomas Charles Terwilliger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Thomas Charles Terwilliger Profile Pages View homepages for scientists and researchers. Explore potential collaborations and project opportunities. Search the extensive range of capabilities by keyword to quickly find who and what you are looking for. submit Thomas Charles Terwilliger Thomas Terwilliger Email Phone (505) 667-0072 Expertise Follow Tom Terwilliger on: ResearchGate LinkedIn Twitter Macromolecular X-ray crystallography - Development of algorithms and software for determining crystal

  9. Proposal Submittal and Scheduling Procedures Entry Page

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Proposal Submittal and Scheduling Procedures for Research at SSRL X-ray/VUV Macromolecular Crystallography SSRL is funded by the Department of Energy, Office of Basic Energy Sciences under contract DE-AC03-76SF00515. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General

  10. Complete Safety Training

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complete Safety Training Print Facility Safety Training Required for ALL Users Users must register with the ALS to obtain an LBNL ID number before they can complete safety training courses. Once registered, choose the non-LDAP login and enter your LBNL ID number to begin. ALS 1001: Safety at the ALS EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B/4 laser EHS 0302 Macromolecular Crystallography Users

  11. Complete Safety Training

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complete Safety Training Print Facility Safety Training Required for ALL Users Users must register with the ALS to obtain an LBNL ID number before they can complete safety training courses. Once registered, choose the non-LDAP login and enter your LBNL ID number to begin. ALS 1001: Safety at the ALS EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B/4 laser EHS 0302 Macromolecular Crystallography Users

  12. Stanford Synchrotron Radiation Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Extension Application for Macromolecular Crystallography Proposals Please submit via email attachment to Lisa Dunn (lisa@slac.stanford.edu) Proposal Number: Date of Extension Request: Spokesperson: 1. PROGRESS: Provide a progress report describing work accomplished at SSRL on this proposal to date (1-2 pages) 2. NEW ELEMENTS: Describe any new elements that may add interest to extending the proposal, if applicable (1-2 paragraphs) 3. FUTURE PLANS: Describe future plans or the next steps that you

  13. Biology Chemistry & Material Science Laboratory 1 | Sample Preparation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Laboratories 1 Cynthia Patty | (650) 926-3925 Biology Chemistry & Material Science Laboratory 1 Inventory The BioChemMat Lab 1 at SSRL is dedicated to researcher experiments, including x-ray absorption and emission spectroscopies, macromolecular crystallography, x-ray scattering, and x-ray imaging. The labs are maintained for final-stage sample preparation and other relatively straight-forward laboratory manipulations. These include buffer preparations, solid sample grinding, solution

  14. Biology Chemistry & Material Science Laboratory 2 | Sample Preparation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Laboratories 2 Cynthia Patty | (650) 926-3925 Biology Chemistry & Material Science Laboratory 2 Inventory The BioChemMat Lab 2 (BCM 2) at SSRL is dedicated to researcher experiments, including x-ray absorption and emission spectroscopies, macromolecular crystallography, x-ray scattering, and x-ray imaging. The labs are maintained for final-stage sample preparation and other relatively straight-forward laboratory manipulations. These include buffer preparations, solid sample grinding,

  15. Complete Safety Training

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complete Safety Training Print Facility Safety Training Required for ALL Users Users must register with the ALS to obtain an LBNL ID number before they can complete safety training courses. Once registered, choose the non-LDAP login and enter your LBNL ID number to begin. ALS 1001: Safety at the ALS EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B/4 laser EHS 0302 Macromolecular Crystallography Users

  16. Complete Safety Training

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complete Safety Training Print Facility Safety Training Required for ALL Users Users must register with the ALS to obtain an LBNL ID number before they can complete safety training courses. Once registered, choose the non-LDAP login and enter your LBNL ID number to begin. ALS 1001: Safety at the ALS EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B/4 laser EHS 0302 Macromolecular Crystallography Users

  17. Complete Safety Training

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complete Safety Training Print Facility Safety Training Required for ALL Users Users must register with the ALS to obtain an LBNL ID number before they can complete safety training courses. Once registered, choose the non-LDAP login and enter your LBNL ID number to begin. ALS 1001: Safety at the ALS EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B/4 laser EHS 0302 Macromolecular Crystallography Users

  18. EA-373-A EDF Trading N.A (MX).pdf

    Office of Environmental Management (EM)

  19. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    SciTech Connect (OSTI)

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; Read, Randy J.; Wiedenheft, Blake

    2015-07-30

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

  20. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; Read, Randy J.; Wiedenheft, Blake

    2015-07-30

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

  1. On the protonation states, hydrogen bonding and catalytic mechanism of family 11 glycosidases: Direct visualization with neutrons

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fisher, Suzanne Zoe; Graham, David E.; Hanson, Leif; Kovalevskyi, Andrii Y.; Langan, Paul; Parks, Jerry M.; Wan, Qun; Ostermann, Andreas; Schrader, Tobias

    2015-10-06

    Most enzymatic reactions involve hydrogen or proton transfer among the enzyme, substrate, and water at physiological pH. Thus, enzyme catalysis cannot be fully understood without accurate mapping of hydrogen atom positions in these macromolecular catalysts. Direct information on the location of hydrogen atoms can be obtained using neutron crystallography. We used neutron crystallography and biomolecular simulation to characterize the initial stage of the glycoside hydrolysis reaction catalyzed by a family 11 glycoside hydrolase. We provide evidence that the catalytic glutamate residue alternates between two conformations bearing different basicities, first to obtain a proton from the bulk solvent, and then tomore » deliver it to the glycosidic oxygen to initiate the hydrolysis reaction.« less

  2. Experimental Station 12-2 | Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2-2 Beamline 12-2 is a PRT station, realized through third party funding from the Gordon and Betty Moore Foundation via the California Institute of Technology and available to general users 60%; it is an undulator beamline with fully adjustable focus from 100 to 15 microns. Micron-sized beams can be achieved by the use of microcollimators. It is optimized for microdiffraction, monochromatic, high-throughput and high-resolution macromolecular crystallography. It is SAD and MAD capable and can be

  3. Vesicle-based method for collecting, manipulating, and chemically processing trace macromolecular species

    DOE Patents [OSTI]

    Davalos, Rafael V.; Ellis, Christopher R. B.

    2010-08-17

    Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

  4. Vesicle-based method and apparatus for collecting, manipulating, and chemically processing trace macromolecular species

    DOE Patents [OSTI]

    Davalos, Rafael V.; Ellis, Christopher R. B.

    2008-03-04

    Disclosed is an apparatus and method for inserting one or several chemical or biological species into phospholipid containers that are controlled within a microfluidic network, wherein individual containers are tracked and manipulated by electric fields and wherein the contained species may be chemically processed.

  5. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

    SciTech Connect (OSTI)

    Brown, Alan; Long, Fei; Nicholls, Robert A.; Toots, Jaan; Emsley, Paul; Murshudov, Garib, E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (United Kingdom)

    2015-01-01

    A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 . Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.

  6. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Hattne, Hattne

    2014-03-04

    Diffraction patterns from thermolysin microcrystals and one dark run, collected in December 2011. This data was used for metrology calibration and general cctbx.xfel development.

  7. Macromolecular organization of the cellulolytic enzyme complex of Clostridium thermocellum as revealed by electron microscopy

    SciTech Connect (OSTI)

    Mayer, F.; Coughlan, M.P.; Mori, Y.; Ljungdahl, L.G.

    1987-12-01

    Clostridium thermocellum JW20 and YM4 both synthesize cellulolytic enzyme complexes, cellulosomes, when grown on medium containing cellulose. In the early stages of cultivation, the cellulosomes from both species exist as tightly packed complexes (tight cellulosomes). These subsequently decompose to loosely packed complexes (loose cellulosomes) and ultimately to free polypeptides. Examination of the loose cellulosomal particles showed that the contain rows of equidistantly spaced, similarly sized polypeptide subunits, with an apparently identical orientation arranged parallel to the major axis of the cellulosome. It is postulated that on binding of a cellulose chain alongside such a row of subunits a simultaneous multicutting event occurs that leads to the release of cellooligosaccharides of four cellobiose units in length (C/sub 4/). Rows of smaller-sized subunits with lower center-to-center distances, which are also present in the cellulosome, subsequently cleave the C/sub 4/ fragments (or cellulose) to C/sub 2/ (cellotetraose) or C/sub 1/ (cellobiose). In this way the cellulosome can catalyze the complete hydrolysis of cellulose.

  8. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    SciTech Connect (OSTI)

    Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de [MPI for Medical Research, Heidelberg (Germany); Brosi, Richard W. W. [Freie Universitat Berlin, Berlin (Germany); Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten [MPI for Medical Research, Heidelberg (Germany); Seidel, Ralf [MPI for Molecular Physiology, Dortmund (Germany); Shoeman, Robert L.; Zimmermann, Sabine [MPI for Medical Research, Heidelberg (Germany); Bittl, Robert [Freie Universitat Berlin, Berlin (Germany); Schlichting, Ilme; Reinstein, Jochen [MPI for Medical Research, Heidelberg (Germany)

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  9. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ibrahim, Mohamed; Chatterjee, Ruchira; Hellmich, Julia; Tran, Rosalie; Bommer, Martin; Yachandra, Vittal K.; Yano, Junko; Kern, Jan; Zouni, Athina

    2015-07-01

    In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup thatmore » requires microcrystals less than 40 μm in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5 Å, using crystals grown without the micro seeding approach, to 4.5 Å using crystals generated with the new method.« less

  10. The crystallography of fatigue crack initiation in Incoloy-908 and A-286 steel

    SciTech Connect (OSTI)

    Krenn, C.R. |

    1996-12-01

    Fatigue crack initiation in the austenitic Fe-Ni superalloys Incoloy-908 and A-286 is examined using local crystallographic orientation measurements. Results are consistent with sharp transgranular initiation and propagation occurring almost exclusively on {l_brace}111{r_brace} planes in Incoloy-908 but on a variety of low index planes in A-286. This difference is attributed to the influence of the semicoherent grain boundary {eta} phase in A-286. Initiation in each alloy occurred both intergranularly and transgranularly and was often associated with blocky surface oxide and carbide inclusions. Taylor factor and resolved shear stress and strain crack initiation hypotheses were tested, but despite an inconclusive suggestion of a minimum required {l_brace}111{r_brace} shear stress, none of the hypotheses were found to convincingly describe preferred initiation sites, even within the subsets of transgranular cracks apparently free from the influence of surface inclusions. Subsurface inclusions are thought to play a significant role in crack initiation. These materials have applications for use in structural conduit for high field superconducting magnets designed for fusion energy use.

  11. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    SciTech Connect (OSTI)

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  12. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechainmore » conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

  13. Direct detection of x-rays for protein crystallography employing a thick, large area CCD

    DOE Patents [OSTI]

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

    An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

  14. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William; Yegian, Derek; Earnest, Thomas N.; Jaklevic, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2005-07-19

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  15. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William F.; Yegian, Derek T.; Earnest, Thomas N.; Jaklevich, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2007-09-25

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  16. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures

    SciTech Connect (OSTI)

    Ibrahim, Mohamed; Chatterjee, Ruchira; Hellmich, Julia; Tran, Rosalie; Bommer, Martin; Yachandra, Vittal K.; Yano, Junko; Kern, Jan; Zouni, Athina

    2015-07-01

    In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup that requires microcrystals less than 40 μm in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5 Å, using crystals grown without the micro seeding approach, to 4.5 Å using crystals generated with the new method.

  17. Processing incommensurately modulated protein diffraction data with Eval15

    SciTech Connect (OSTI)

    Porta, Jason [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Lovelace, Jeffrey J. [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Borgstahl, Gloria E. O., E-mail: gborgstahl@unmc.edu [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States)

    2011-07-01

    Data processing of an incommensurately modulated profilinactin crystal is described. Recent challenges in biological X-ray crystallography include the processing of modulated diffraction data. A modulated crystal has lost its three-dimensional translational symmetry but retains long-range order that can be restored by refining a periodic modulation function. The presence of a crystal modulation is indicated by an X-ray diffraction pattern with periodic main reflections flanked by off-lattice satellite reflections. While the periodic main reflections can easily be indexed using three reciprocal-lattice vectors a*, b*, c*, the satellite reflections have a non-integral relationship to the main lattice and require a q vector for indexing. While methods for the processing of diffraction intensities from modulated small-molecule crystals are well developed, they have not been applied in protein crystallography. A recipe is presented here for processing incommensurately modulated data from a macromolecular crystal using the Eval program suite. The diffraction data are from an incommensurately modulated crystal of profilinactin with single-order satellites parallel to b*. The steps taken in this report can be used as a guide for protein crystallographers when encountering crystal modulations. To our knowledge, this is the first report of the processing of data from an incommensurately modulated macromolecular crystal.

  18. Collaborative Computational Project for Electron cryo-Microscopy

    SciTech Connect (OSTI)

    Wood, Chris; Burnley, Tom [Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom); Patwardhan, Ardan [European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Scheres, Sjors [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Topf, Maya [University of London, Malet Street, London WC1E 7HX (United Kingdom); Roseman, Alan [University of Manchester, Oxford Road, Manchester M13 9PT (United Kingdom); Winn, Martyn, E-mail: martyn.winn@stfc.ac.uk [Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom)

    2015-01-01

    The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed.

  19. RapiData: a Practical Course in Macromolecular X-ray Diffraction Data Measurement and Structure Solving at the NSLS

    SciTech Connect (OSTI)

    Sweet, R.; Soares, A

    2010-01-01

    RapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. Students are invited to bring their own research projects for measurement, and about half of them do. The students frequently solve half a dozen structures during the course. Tutorials by the lecturers run throughout the data-collection period. The crystal-preparation laboratory is popular for tutorials and practice, and often there is a beamline available for practice. This article provides details about the organization of the course and tells some of the reasons for its success.

  20. The carburization of transition metal molybdates (MxMoO₄, M= Cu, Ni or Co) and the generation of highly active metal/carbide catalysts for CO₂ hydrogenation

    SciTech Connect (OSTI)

    Rodriguez, Jose A.; Xu, Wenqian; Ramirez, Pedro J.; Stachiola, Dario; Brito, Joaquin L.

    2015-05-06

    A new approach has been tested for the preparation of metal/Mo₂C catalysts using mixed-metal oxide molybdates as precursors. Synchrotron-based in situ time-resolved X-ray diffraction was used to study the reduction and carburization processes of Cu₃(MoO₄)₂(OH)₂, a-NiMoO₄ and CoMoO₄•nH₂O by thermal treatment under mixtures of hydrogen and methane. In all cases, the final product was β-Mo₂C and a metal phase (Cu, Ni, or Co), but the transition sequence varied with the different metals, and it could be related to the reduction potential of the Cu²⁺, Ni²⁺ and Co²⁺ cations inside each molybdate. The synthesized Cu/Mo₂C, Ni/Mo₂C and Co/Mo₂C catalysts were highly active for the hydrogenation of CO₂. The metal/Mo₂C systems exhibited large variations in the selectivity towards methanol, methane and CnH₂n₊₂ (n > 2) hydrocarbons depending on the nature of the supported metal and its ability to cleave C-O bonds. Cu/Mo₂C displayed a high selectivity for CO and methanol production. Ni/Mo₂C and Co/Mo₂C were the most active catalysts for the activation and full decomposition of CO₂, showing high selectivity for the production of methane (Ni case) and CnH₂n₊₂ (n > 2) hydrocarbons (Co case).

  1. The carburization of transition metal molybdates (MxMoO?, M= Cu, Ni or Co) and the generation of highly active metal/carbide catalysts for CO? hydrogenation

    SciTech Connect (OSTI)

    Rodriguez, Jose A.; Xu, Wenqian; Ramirez, Pedro J.; Stachiola, Dario; Brito, Joaquin L.

    2015-05-06

    A new approach has been tested for the preparation of metal/Mo?C catalysts using mixed-metal oxide molybdates as precursors. Synchrotron-based in situ time-resolved X-ray diffraction was used to study the reduction and carburization processes of Cu?(MoO?)?(OH)?, a-NiMoO? and CoMoO?nH?O by thermal treatment under mixtures of hydrogen and methane. In all cases, the final product was ?-Mo?C and a metal phase (Cu, Ni, or Co), but the transition sequence varied with the different metals, and it could be related to the reduction potential of the Cu?, Ni? and Co? cations inside each molybdate. The synthesized Cu/Mo?C, Ni/Mo?C and Co/Mo?C catalysts were highly active for the hydrogenation of CO?. The metal/Mo?C systems exhibited large variations in the selectivity towards methanol, methane and CnH?n?? (n > 2) hydrocarbons depending on the nature of the supported metal and its ability to cleave C-O bonds. Cu/Mo?C displayed a high selectivity for CO and methanol production. Ni/Mo?C and Co/Mo?C were the most active catalysts for the activation and full decomposition of CO?, showing high selectivity for the production of methane (Ni case) and CnH?n?? (n > 2) hydrocarbons (Co case).

  2. The carburization of transition metal molybdates (MxMoO₄, M= Cu, Ni or Co) and the generation of highly active metal/carbide catalysts for CO₂ hydrogenation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rodriguez, Jose A.; Xu, Wenqian; Ramirez, Pedro J.; Stachiola, Dario; Brito, Joaquin L.

    2015-05-06

    A new approach has been tested for the preparation of metal/Mo₂C catalysts using mixed-metal oxide molybdates as precursors. Synchrotron-based in situ time-resolved X-ray diffraction was used to study the reduction and carburization processes of Cu₃(MoO₄)₂(OH)₂, a-NiMoO₄ and CoMoO₄•nH₂O by thermal treatment under mixtures of hydrogen and methane. In all cases, the final product was β-Mo₂C and a metal phase (Cu, Ni, or Co), but the transition sequence varied with the different metals, and it could be related to the reduction potential of the Cu²⁺, Ni²⁺ and Co²⁺ cations inside each molybdate. The synthesized Cu/Mo₂C, Ni/Mo₂C and Co/Mo₂C catalysts were highlymore » active for the hydrogenation of CO₂. The metal/Mo₂C systems exhibited large variations in the selectivity towards methanol, methane and CnH₂n₊₂ (n > 2) hydrocarbons depending on the nature of the supported metal and its ability to cleave C-O bonds. Cu/Mo₂C displayed a high selectivity for CO and methanol production. Ni/Mo₂C and Co/Mo₂C were the most active catalysts for the activation and full decomposition of CO₂, showing high selectivity for the production of methane (Ni case) and CnH₂n₊₂ (n > 2) hydrocarbons (Co case).« less

  3. Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography [Neutron and ultrahigh resolution X-ray crystallography reveals water as the proton donor in the catalytic mechanism of dihydrofolate reductase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wan, Qun; Bennett, Brad C.; Wilson, Mark A.; Kovalevsky, Andrey; Langan, Paul; Howell, Elizabeth E.; Dealwis, Chris

    2014-12-01

    Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to the lack of consensus on a catalytic mechanism. To resolve this ambiguity, we conducted neutron and ultrahigh resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of DHFR with folate and NADP+ from E. coli. The neutron data were collected to 2.0 Å resolution using a 3.6 mm3 crystal with the quasi-Laue technique, and the structuremore » reveals that the N3 atom of folate is protonated while Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer due to protonation of the N3 atom, suggesting tautomerization is unnecessary for catalysis. In the 1.05 Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa of the N5 atom of DHF by Asp27, and protonation of N5 by water whose access to the active site is gated by fluctuation of the Met20 side chain even though the Met-20 loop is closed.« less

  4. Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography [Neutron and ultrahigh resolution X-ray crystallography reveals water as the proton donor in the catalytic mechanism of dihydrofolate reductase

    SciTech Connect (OSTI)

    Wan, Qun; Bennett, Brad C.; Wilson, Mark A.; Kovalevsky, Andrey; Langan, Paul; Howell, Elizabeth E.; Dealwis, Chris

    2014-12-01

    Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to the lack of consensus on a catalytic mechanism. To resolve this ambiguity, we conducted neutron and ultrahigh resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of DHFR with folate and NADP+ from E. coli. The neutron data were collected to 2.0 Å resolution using a 3.6 mm3 crystal with the quasi-Laue technique, and the structure reveals that the N3 atom of folate is protonated while Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer due to protonation of the N3 atom, suggesting tautomerization is unnecessary for catalysis. In the 1.05 Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa of the N5 atom of DHF by Asp27, and protonation of N5 by water whose access to the active site is gated by fluctuation of the Met20 side chain even though the Met-20 loop is closed.

  5. Supporting Advanced Scientific Computing Research * Basic Energy...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Peeringupgrades: * EQX-SJ:installedMX480onOct15 th * EQX-ASH:installedMX480onNov30 th * EQX-CHI:PendingMX480ins...

  6. Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

    SciTech Connect (OSTI)

    Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Zuo, Xiaobing; Noll, Bruce C.

    2015-04-15

    Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the nanostructure problem. Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.

  7. Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

    SciTech Connect (OSTI)

    Gardberg, Anna S.; Del Castillo, Alexis R.; Weiss, Kevin L.; Meilleur, Flora; Blakeley, Matthew P.; Myles, Dean A.A.

    2010-11-19

    The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 {angstrom} resolution neutron diffraction studies of fully perdeuterated and selectively CH{sub 3}-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 {angstrom} resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the {sigma} level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 {angstrom} resolution RT neutron data for perdeuterated rubredoxin are {approx}8 times more likely overall to provide high-confidence positions for D atoms than 1.1 {angstrom} resolution X-ray data at 100 K or RT. At or above the 1.0{sigma} level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 {angstrom} resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0{sigma} level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

  8. Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Shen, Xiao; Hernandez-Pagan, Emil; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo Tapia, Juan Carlos; Macdonald, Janet; Pennycook, Stephen J.; Pantelides, Sokrates T.

    2014-11-14

    The search for optimal thermoelectric materials aims for structures in which the crystalline order is disrupted to lower the thermal conductivity without degradation of the electron conductivity. Here we report the synthesis and characterization of ternary nanoparticles (two cations and one anion) that exhibit a new form of crystal-line order: an uninterrupted, perfect, global Bravais lattice, in which the two cations exhibit a wide array of distinct ordering patterns within the cation sublattice, form-ing interlaced domains and phases. Partitioning into domains and phases is not unique; the corresponding boundaries have no structural defects or strain and entail no energy cost.more » We call this form of crystalline order “interlaced crystals” and present the example of hexagonal-CuInS2. Interlacing is possible in multi-cation tetrahedral-ly-bonded compound with an average of two electrons per bond. Interlacing has min-imal effect on electronic properties, but should strongly reduce phonon transport, making interlaced crystals attractive for thermoelectric applications.« less

  9. Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography

    SciTech Connect (OSTI)

    Shen, Xiao; Hernandez-Pagan, Emil; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo Tapia, Juan Carlos; Macdonald, Janet; Pennycook, Stephen J.; Pantelides, Sokrates T.

    2014-11-14

    The search for optimal thermoelectric materials aims for structures in which the crystalline order is disrupted to lower the thermal conductivity without degradation of the electron conductivity. Here we report the synthesis and characterization of ternary nanoparticles (two cations and one anion) that exhibit a new form of crystal-line order: an uninterrupted, perfect, global Bravais lattice, in which the two cations exhibit a wide array of distinct ordering patterns within the cation sublattice, form-ing interlaced domains and phases. Partitioning into domains and phases is not unique; the corresponding boundaries have no structural defects or strain and entail no energy cost. We call this form of crystalline order “interlaced crystals” and present the example of hexagonal-CuInS2. Interlacing is possible in multi-cation tetrahedral-ly-bonded compound with an average of two electrons per bond. Interlacing has min-imal effect on electronic properties, but should strongly reduce phonon transport, making interlaced crystals attractive for thermoelectric applications.

  10. Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect (OSTI)

    Lewis, H.A.; Wang, C.; Zhao, X.; Hamuro, Y.; Conners, K.; Kearins, M.C.; Lu, F.; Sauder, J.M.; Molnar, K.S.; Coales, S.J.; Maloney, P.C.; Guggino, W.B.; Wetmore, D.R.; Weber, P.C.; Hunt, J.F. (SGX); (ExSAR); (Cystic); (JHU-MED); (Columbia)

    2012-04-30

    The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.

  11. Correlated Single-Crystal Electronic Absorption Spectroscopy and X-ray Crystallography at NSLS Beamline X26-C

    SciTech Connect (OSTI)

    A Orville; R Buono; M Cowan; A Heroux; G Shea-McCarthy; D Schneider; J Skinner; M Skinner; D Stoner-Ma; R Sweet

    2011-12-31

    The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

  12. Towards phasing using high X-ray intensity

    SciTech Connect (OSTI)

    Galli, Lorenzo; Son, Sang-Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sébastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; Nass, Karol; Shoeman, Robert L.; Timneanu, Nicusor; Santra, Robin; Schlichting, Ilme; Chapman, Henry N.

    2015-09-30

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

  13. 2010 Diffraction Methods in Structural Biology

    SciTech Connect (OSTI)

    Dr. Ana Gonzalez

    2011-03-10

    Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oral or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.

  14. Towards phasing using high X-ray intensity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Galli, Lorenzo; Son, Sang -Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sébastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; et al

    2015-09-30

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. In conclusion, a pattern sorting schememore » is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.« less

  15. Challenges and solutions for the analysis of in situ , in crystallo micro-spectrophotometric data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dworkowski, Florian S. N.; Hough, Michael A.; Pompidor, Guillaume; Fuchs, Martin R.

    2015-01-01

    Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the presentmore » article, we discuss how to characterize and treat these sample-dependent artefacts in a reproducible manner and we demonstrate the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox.« less

  16. Station for X-ray structural analysis of materials and single crystals (including nanocrystals) on a synchrotron radiation beam from the wiggler at the Siberia-2 storage ring

    SciTech Connect (OSTI)

    Kheiker, D. M. Kovalchuk, M. V.; Korchuganov, V. N.; Shilin, Yu. N.; Shishkov, V. A.; Sulyanov, S. N.; Dorovatovskii, P. V.; Rubinsky, S. V.; Rusakov, A. A.

    2007-11-15

    The design of the station for structural analysis of polycrystalline materials and single crystals (including nanoobjects and macromolecular crystals) on a synchrotron radiation beam from the superconducting wiggler of the Siberia-2 storage ring is described. The wiggler is constructed at the Budker Institute of Nuclear Physics of the Siberian Division of the Russian Academy of Sciences. The X-ray optical scheme of the station involves a (1, -1) double-crystal monochromator with a fixed position of the monochromatic beam and a sagittal bending of the second crystal, segmented mirrors bent by piezoelectric motors, and a (2{theta}, {omega}, {phi}) three-circle goniometer with a fixed tilt angle. Almost all devices of the station are designed and fabricated at the Shubnikov Institute of Crystallography of the Russian Academy of Sciences. The Bruker APEX11 two-dimensional CCD detector will serve as a detector in the station.

  17. Towards phasing using high X-ray intensity

    SciTech Connect (OSTI)

    Galli, Lorenzo; Son, Sang -Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sébastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; Nass, Karol; Shoeman, Robert L.; Timneanu, Nicusor; Santra, Robin; Schlichting, Ilme; Chapman, Henry N.

    2015-09-30

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. In conclusion, a pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

  18. Browse by Discipline -- E-print Network Subject Pathways: --...

    Office of Scientific and Technical Information (OSTI)

    ... Crystallography Laboratory, National Cancer Institute Waxman, David J. (David J. ... Crystallography Laboratory, National Cancer Institute Wohrer, Adrien (Adrien Wohrer) ...

  19. Structural snapshots along the reaction pathway of Yersinia pestis...

    Office of Scientific and Technical Information (OSTI)

    ... Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: ... Copyright (c) International Union of Crystallography 2014; Country of input: International ...

  20. Femtosecond X-ray protein nanocrystallography

    SciTech Connect (OSTI)

    Chapman, Henry N.; Barty, Anton; White, Thomas A.; Aquila, Andrew; Schulz, Joachim; DePonte, Daniel P.; Martin, Andrew V.; Coppola, Nicola; Liang, Mengning; Caleman, Carl; Gumprecht, Lars; Stern, Stephan; Nass, Karol; Fromme, Petra; Hunter, Mark S.; Grotjohann, Ingo; Fromme, Raimund; Kirian, Richard A.; Weierstall, Uwe; Doak, R. Bruce; Schmidt, Kevin E.; Wang, Xiaoyu; Spence, John C. H.; Schlichting, Ilme; Epp, Sascha W.; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Strüder, Lothar; Ullrich, Joachim; Krasniqi, Faton; Lomb, Lukas; Shoeman, Robert L.; Bott, Mario; Barends, Thomas R. M.; Kuhnel, Kai-Uwe; Schroter, Claus-Dieter; Hartmann, Robert; Holl, Peter; Reich, Christian; Soltau, Heike; Kimmel, Nils; Weidenspointner, Georg; Pietschner, Daniel; Hauser, Günter; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Andritschke, Robert; Boutet, Sébastien; Krzywinski, Jacek; Bostedt, Christoph; Messerschmidt, Marc; Bozek, John D.; Williams, Garth J.; Bogan, Michael J.; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Gorke, Hubert; Hau-Riege, Stefan P.; Frank, Matthias; Maia, Filipe R. N. C.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Holton, James M.; Marchesini, Stefano; Neutze, Richard; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Barthelmess, Miriam; Bajt, Saša; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn

    2011-02-03

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  1. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    SciTech Connect (OSTI)

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  2. Improving experimental phases for strong reflections prior to density modification

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-09-20

    Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number ofmore » strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

  3. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  4. An evaluation of adhesive sample holders for advanced crystallographic experiments

    SciTech Connect (OSTI)

    Mazzorana, Marco; Sanchez-Weatherby, Juan Sandy, James; Lobley, Carina M. C.; Sorensen, Thomas

    2014-09-01

    Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-controlled studies is investigated. The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.

  5. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: insights from x-ray crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kumaran, D.; Adler, M.; Levit, M.; Krebs, M.; Sweeney, R.; Swaminathan, S.

    2015-10-17

    The seven antigenically distinct serotypes (A to G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins: the heavy chain is responsible for neurospecific binding, internalization and translocation, and the light chain is responsible for substrate cleavage. Because of their extreme toxicity and prior history of weaponization, the BoNTs are considered to be potential bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than critical care;more » therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was synthesized and found to inhibit BoNT/A light chain (Balc) with high affinity. When tested in a cell-free Förster resonance excitation transfer (FRET) assay, CPI-1 was found to have a Ki of 13.9 nM using full-length Balc448 and 42.1 nM using a truncated crystallizable form of light chain (Balc424). Co-crystallization of CPI-1 with Balc424 revealed that in the Balc-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn2+ binding region involved in catalysis. This is in contrast to linear peptide inhibitors described to date which block only the latter« less

  6. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: insights from x-ray crystallography

    SciTech Connect (OSTI)

    Kumaran, D.; Adler, M.; Levit, M.; Krebs, M.; Sweeney, R.; Swaminathan, S.

    2015-10-17

    The seven antigenically distinct serotypes (A to G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins: the heavy chain is responsible for neurospecific binding, internalization and translocation, and the light chain is responsible for substrate cleavage. Because of their extreme toxicity and prior history of weaponization, the BoNTs are considered to be potential bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than critical care; therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was synthesized and found to inhibit BoNT/A light chain (Balc) with high affinity. When tested in a cell-free Förster resonance excitation transfer (FRET) assay, CPI-1 was found to have a Ki of 13.9 nM using full-length Balc448 and 42.1 nM using a truncated crystallizable form of light chain (Balc424). Co-crystallization of CPI-1 with Balc424 revealed that in the Balc-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn2+ binding region involved in catalysis. This is in contrast to linear peptide inhibitors described to date which block only the latter

  7. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vandavasi, Venu Gopal; Weiss, Kevin L.; Cooper, Jonathan B.; Erskine, Peter T.; Tomanicek, Stephen J.; Ostermann, Andreas; Schrader, Tobias E.; Ginell, Stephan L.; Coates, Leighton

    2015-12-02

    The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacksmore » a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.« less

  8. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

    SciTech Connect (OSTI)

    Vandavasi, Venu Gopal; Weiss, Kevin L.; Cooper, Jonathan B.; Erskine, Peter T.; Tomanicek, Stephen J.; Ostermann, Andreas; Schrader, Tobias E.; Ginell, Stephan L.; Coates, Leighton

    2015-12-02

    The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.

  9. Structure of a complex of uridine phosphorylase from Yersinia pseudotuberculosis with the modified bacteriostatic antibacterial drug determined by X-ray crystallography and computer analysis

    SciTech Connect (OSTI)

    Balaev, V. V.; Lashkov, A. A. Gabdoulkhakov, A. G.; Seregina, T. A.; Dontsova, M. V.; Mikhailov, A. M.

    2015-03-15

    Pseudotuberculosis and bubonic plague are acute infectious diseases caused by the bacteria Yersinia pseudotuberculosis and Yersinia pestis. These diseases are treated, in particular, with trimethoprim and its modified analogues. However, uridine phosphorylases (pyrimidine nucleoside phosphorylases) that are present in bacterial cells neutralize the action of trimethoprim and its modified analogues on the cells. In order to reveal the character of the interaction of the drug with bacterial uridine phosphorylase, the atomic structure of the unligated molecule of uridine-specific pyrimidine nucleoside phosphorylase from Yersinia pseudotuberculosis (YptUPh) was determined by X-ray diffraction at 1.7 Å resolution with high reliability (R{sub work} = 16.2, R{sub free} = 19.4%; r.m.s.d. of bond lengths and bond angles are 0.006 Å and 1.005°, respectively; DPI = 0.107 Å). The atoms of the amino acid residues of the functionally important secondary-structure elements—the loop L9 and the helix H8—of the enzyme YptUPh were located. The three-dimensional structure of the complex of YptUPh with modified trimethoprim—referred to as 53I—was determined by the computer simulation. It was shown that 53I is a pseudosubstrate of uridine phosphorylases, and its pyrimidine-2,4-diamine group is located in the phosphate-binding site of the enzyme YptUPh.

  10. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destructio...

  11. Search for: All records | SciTech Connect

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    and superfluidity (1) crystallography (1) crystals (1) electron beams (1) ... 68 in the International Tables for Crystallography) at 315K. A very fine twin structure ...

  12. Center for Nanophase Materials Sciences (CNMS) - General Characterizat...

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    of evolved gases See Macromolecular Nanomaterials Capabilities Differential Scanning Calorimeter TA Instruments Q2000 with temperature range from -180 to 550C See Macromolecular...

  13. Beamline 9.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    disciplines: Applied science, biology, polymers, soft materials. Endstations: Serial crystallography Diffractive imaging Nanosurveyor GENERAL BEAMLINE INFORMATION...

  14. Covering complete proteomes with X-ray structures: A current snapshot

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

  15. Covering complete proteomes with X-ray structures: A current snapshot

    SciTech Connect (OSTI)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  16. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data

    SciTech Connect (OSTI)

    Dworkowski, Florian S. N.; Hough, Michael A.; Pompidor, Guillaume

    2015-01-01

    The particular challenge of the analysis of optical absorption and Raman spectroscopic data measured from protein crystals and how the SLS-APE software toolbox supports scientists in dealing with such data is described. Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APEin situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.

  17. High-pressure crystallography and compression behavior of the alkali-scandium-germanate end-members LiScGe{sub 2}O{sub 6} and NaScGe{sub 2}O{sub 6}

    SciTech Connect (OSTI)

    Hofer, Gregor; Redhammer, Günther; Miletich, Ronald

    2015-09-15

    Synthetic single-crystal samples of the monoclinic pyroxene-type compounds LiScGe{sub 2}O{sub 6} and NaScGe{sub 2}O{sub 6} have been investigated by means of in-situ high-pressure Raman spectroscopy and X-ray diffraction techniques. Crystal-structure investigations at hydrostatic high-pressure conditions were carried out in addition to 10{sup −4} GPa measurements using the diamond-anvil cell technique up to ∼9.5 GPa. Both samples, LiScGe{sub 2}O{sub 6} (space group P2{sub 1}/c, a=9.9999(8) Å, b=9.1040(2) Å, c=5.4610(2) Å, β=109.240(2)° at 10{sup −4} GPa) and NaScGe{sub 2}O{sub 6} (space group C2/c, a=10.1678(5) Å, b=9.1583(5) Å, c=5.5672(3) Å, β=107.257(3)° at 10{sup −4} GPa), did not undergo any compression-induced change of symmetry as confirmed by single-crystal diffraction patterns. Series of high-pressure Raman spectra confirm the absence of any symmetry-related structural phase transition with band positions shifting in a smooth fashion on increasing pressure. High-precision lattice parameters, as determined from X-ray diffraction profile analyzes, were used to monitor both the compressibilities of lattice directions and the evolution of the unit-cell volume with pressure. The experimental data was fitted using a third-order Birch–Murnaghan equation-of-state approach and parameterized fits yield V{sub 0}=469.60(11) Å{sup 3}, K{sub 0}=85.6(1.3) GPa and K′=5.9(4) for LiScGe{sub 2}O{sub 6} and V{sub 0}=495.95(19) Å{sup 3}, K{sub 0}=79(3) GPa and K′=3.9(1.1) for NaScGe{sub 2}O{sub 6}. The systematic comparison of volume properties and compression behavior shows that both pyroxene-type compounds follow established trend lines with similar slopes in comparing volumes versus bulk moduli, and confirm that the position of trend lines in this systematics describing variations with M1 critically depend on the type of M2 and T cations, independent on the space-group symmetry. - Graphical abstract: Polyhedral model of the LiScGe{sub 2}O{sub 6} crystal structure at 9.51 GPa. Red and blue: crystallographic distinctive germanium-tetrahedral chains; Green: scandium-octahedral chains; Purple: lithium atoms. - Highlights: • High-quality high-pressure data of previously uninvestigated germanate compounds. • Results confirmed through complementing sXRD with Raman spectroscopy. • Comparison and relation of high-pressure pyroxene-type compounds.

  18. Crystallography and Physical Properties of BaCo2As2, Ba0.94K0.06Co2As2, and Ba0.78K0.22Co2As2

    SciTech Connect (OSTI)

    Anand, V K; Quirinale, Dante G; Lee, Yongbin; Harmon, Bruce N; Furukawa, Yuji; Ogloblichev, V V; Huq, A; Abernathy, D L; Stephens, P W; McQueeney, Robert J; Kreyssig, Aandreas; Goldman, Alan I; Johnston, David C

    2014-08-01

    The crystallographic and physical properties of polycrystalline and single crystal samples of BaCo2As2 and K-doped Ba{1-x}K{x}Co2As2 (x = 0.06, 0.22) are investigated by x-ray and neutron powder diffraction, magnetic susceptibility chi, magnetization, heat capacity Cp, {75}As NMR and electrical resistivity rho measurements versus temperature T. The crystals were grown using both Sn flux and CoAs self-flux, where the Sn-grown crystals contain 1.6-2.0 mol% Sn. All samples crystallize in the tetragonal ThCr2Si2-type structure (space group I4/mmm). For BaCo2As2, powder neutron diffraction data show that the c-axis lattice parameter exhibits anomalous negative thermal expansion from 10 to 300 K, whereas the a-axis lattice parameter and the unit cell volume show normal positive thermal expansion over this T range. No transitions in BaCo2As2 were found in this T range from any of the measurements. Below 40-50 K, we find rho ~ T^2 indicating a Fermi liquid ground state. A large density of states at the Fermi energy D(EF) ~ 18 states/(eV f.u.) for both spin directions is found from low-T Cp(T) measurements, whereas the band structure calculations give D(EF) = 8.23 states/(eV f.u.). The {75}As NMR shift data versus T have the same T dependence as the chi(T) data, demonstrating that the derived chi(T) data are intrinsic. The observed {75}As nuclear spin dynamics are consistent with the presence of ferromagnetic and/or stripe-type antiferromagnetic spin fluctuations. The crystals of Ba{0.78}K{0.22}Co2As2 were grown in Sn flux and show properties very similar to those of undoped BaCo2As2. On the other hand, the crystals from two batches of Ba{0.94}K{0.06}Co2As2 grown in CoAs self-flux show evidence of weak ferromagnetism at T < 10 K with small ordered moments at 1.8 K of 0.007 and 0.03 muB per formula unit, respectively.

  19. Holistic data analysis and modeling poised to transform protein...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein X-ray crystallography Holistic data analysis and modeling poised to transform protein X-ray crystallography A new 3-D modeling and data-extraction technique is about to ...

  20. Microbial Electrolysis Cells (MECs) for High Yield Hydrogen ...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Microbial Electrochemical Technology (MxCs): Challenges and Opportunities 2013 Biological Hydrogen Production Workshop Summary Report Hydrogen and Biogas Production using Microbial ...

  1. EA-406 Sempra Generation, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-406 Sempra Generation, LLC Order authoriizing Sempra Generation, LLC to export electric energy to Mexico. PDF icon EA-406 Sempra Generation (MX).pdf More Documents & ...

  2. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    2013 Structural Insight into HIV-1 Restriction by MxB Fribourgh, Jennifer L. ; Nguyen, Henry C. ; Matreyek, Kenneth A. ; Alvarez, Frances Joan D. ; Summers, Brady J. ; Dewdney, ...

  3. Beam Stability Complaint Form

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    For New Users For Current Users For Administrators MX Users APS User Portal APS Data Management Practices Find a Beamline Apply for Beam Time ESAF Contacts Calendars User...

  4. Synthesis and structure of a 2D → 3D framework with coexistence...

    Office of Scientific and Technical Information (OSTI)

    Monitoring and Pollution Control, Collaborative Innovation ... Crystallography Reports; Journal Volume: 60; Journal Issue: ... Country of input: International Atomic Energy Agency ...

  5. Beamline 5.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes...

  6. Beamline 9.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 Print Diffraction Microscopy Scientific disciplines: Applied science, biology, polymers, soft materials. Endstations: Serial crystallography Diffractive imaging Nanosurveyor...

  7. Beamline 9.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    0.1 Print Diffraction Microscopy Scientific disciplines: Applied science, biology, polymers, soft materials. Endstations: Serial crystallography Diffractive imaging Nanosurveyor...

  8. 391st Brookhaven Lecture

    ScienceCinema (OSTI)

    Bob Sweet

    2010-09-01

    A description of how crystallography methods work and how several results obtained using the NSLS have impacted biological science.

  9. Beamline 5.0.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural biology ...

  10. xMDFF: molecular dynamics flexible fitting of low-resolution...

    Office of Scientific and Technical Information (OSTI)

    ... Country of Publication: Denmark Language: English Subject: 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; CRYSTALS; ...

  11. Crystal structure of Sr{sub 3}Ir{sub 2}O{sub 7} investigated...

    Office of Scientific and Technical Information (OSTI)

    Agency (IAEA) Country of Publication: United States Language: English Subject: 36 MATERIALS SCIENCE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ELECTRON DIFFRACTION; FERROMAGNETISM; ...

  12. Beamline 9.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Print Diffraction Microscopy Scientific disciplines: Applied science, biology, polymers, soft materials. Endstations: Serial crystallography Diffractive imaging Nanosurveyor...

  13. 391st Brookhaven Lecture

    SciTech Connect (OSTI)

    Bob Sweet

    2004-02-25

    A description of how crystallography methods work and how several results obtained using the NSLS have impacted biological science.

  14. Covering complete proteomes with X-ray structures: a current snapshot

    SciTech Connect (OSTI)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-11-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  15. CrowdPhase: crowdsourcing the phase problem

    SciTech Connect (OSTI)

    Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

    2014-06-01

    The idea of attacking the phase problem by crowdsourcing is introduced. Using an interactive, multi-player, web-based system, participants work simultaneously to select phase sets that correspond to better electron-density maps in order to solve low-resolution phasing problems. The human mind innately excels at some complex tasks that are difficult to solve using computers alone. For complex problems amenable to parallelization, strategies can be developed to exploit human intelligence in a collective form: such approaches are sometimes referred to as ‘crowdsourcing’. Here, a first attempt at a crowdsourced approach for low-resolution ab initio phasing in macromolecular crystallography is proposed. A collaborative online game named CrowdPhase was designed, which relies on a human-powered genetic algorithm, where players control the selection mechanism during the evolutionary process. The algorithm starts from a population of ‘individuals’, each with a random genetic makeup, in this case a map prepared from a random set of phases, and tries to cause the population to evolve towards individuals with better phases based on Darwinian survival of the fittest. Players apply their pattern-recognition capabilities to evaluate the electron-density maps generated from these sets of phases and to select the fittest individuals. A user-friendly interface, a training stage and a competitive scoring system foster a network of well trained players who can guide the genetic algorithm towards better solutions from generation to generation via gameplay. CrowdPhase was applied to two synthetic low-resolution phasing puzzles and it was shown that players could successfully obtain phase sets in the 30° phase error range and corresponding molecular envelopes showing agreement with the low-resolution models. The successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it

  16. Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy

    SciTech Connect (OSTI)

    Wallace, B.

    2009-01-01

    Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational

  17. Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

    SciTech Connect (OSTI)

    Chaikuad, Apirat; Knapp, Stefan; Delft, Frank von

    2015-07-28

    An alternative strategy for PEG sampling is suggested through the use of four newly defined PEG smears to enhance chemical space in reduced screens with a benefit towards protein crystallization. The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.

  18. IUPAC_handout

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    Prof. Paula Hammond, Massachusetts Institute of Technology Macromolecules in Biotechnology and Medicine Prof. Buddy Ratner, University of Washington Complex Macromolecular...

  19. Beamline 5.3.2.2

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    size at sample (FWHM) 25 nm (theoretical), 31 nm actual Scientific applications Photovoltaics, thin films, macromolecular chemistry, geology, cosmological chemistry,...

  20. Links

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    Useful Links BIOSYNC: Structural Biology Synchrotron Users Organization X-ray Anomalous Scattering Going MAD at CHESS Protein Data Bank Protein Data Bank Search International Union of Crystallography American Crystallographic Association Crystallography 101 Teaching Crystallography Periodic Table Periodic Table and X-ray Properties X-ray data booklet Merohedral crystal twinning server Software Links CCP4 MOSFLM HKL Research, Inc. homepage Solve/Resolve The O-files - Useful reference to the O

  1. What Triggers Asthma - Newcomer

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    PROTEIN CRYSTALLOGRAPHY (PX): determine molecular structures with x-ray diffraction a protein crystal is a uniform array of individual proteins Prepare crystals of the...

  2. Beamline 5.0.2

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    2 Print Berkeley Center for Structural Biology (BCSB) Multiple-wavelength anomalous diffraction (MAD) and monochromatic protein crystallography Scientific discipline: Structural...

  3. Search for: All records | SciTech Connect

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    Accurate Nanoscale Crystallography in Real-Space Using Scanning Transmission Electron ... Furthermore, we apply nanoscale electron diffraction methods to visualize the crystal ...

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    ... (IE) (United States) USDOE Office of Intelligence and Counterintelligence (IN) (United ... changes in crystallography, step edges and boundaries between the multiple sub-lattices. ...

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    Everything2 Electronic Full Text0 Citations2 Multimedia0 Datasets0 Software0 Filter Results Filter by Subject crystallography (1) ferromagnetic shape memory alloy (1) heusler ...

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    (2) crystallography (2) diseases (2) gtp-ases (2) hormones (2) morphine (2) particle accelerators (2) receptors (2) Filter by Author Weis, William I. (39) Kobilka, Brian K. ...

  7. Automatic recovery of missing amplitudes and phases in tilt-limited...

    Office of Scientific and Technical Information (OSTI)

    Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals Citation Details In-Document Search Title: Automatic...

  8. Beamline 5.0.3

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    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes...

  9. Beamline 5.0.3

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Beamline 5.0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION...

  10. Synthesis, crystal, and biological activity of a novel carbene...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Synthesis, crystal, and ... Resource Type: Journal Article Resource Relation: Journal Name: Crystallography Reports; Journal Volume: ...

  11. Synthesis, spectral characterization, and single crystal structure...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Synthesis, spectral ... Resource Type: Journal Article Resource Relation: Journal Name: Crystallography Reports; Journal Volume: ...

  12. De novo protein crystal structure determination from X-ray free-electron laser data

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Barends, Thomas, R.M.

    2013-11-25

    Serial femtosecond crystallography (SFX) data of microcrystals of a lysozyme gadolinium derivative. The data was used to demonstrate de-novo phasing by single anomalous dispersion.

  13. Robust, High-Throughput Analysis of Protein Structures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    three-dimensional shape. Although x-ray crystallography yields higher-resolution images, SAXS makes up for what it lacks in precision by providing fast, accurate...

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    ... Filter Results Filter by Subject acetylation (1) applied life sciences (1) basic biological sciences (1) chromatin (1) crystallography (1) dimers (1) heat-shock proteins (1) ...

  15. Structure and Histone Binding Properties of the Vps75-Rtt109...

    Office of Scientific and Technical Information (OSTI)

    Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ACETYLATION; CHROMATIN; CRYSTALLOGRAPHY; DIMERS; HEAT-SHOCK PROTEINS; HISTONES; LYSINE; MODIFICATIONS; PROTEIN ...

  16. Beamline 9.0.1

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    9.0.1 Print Diffraction Microscopy Scientific disciplines: Applied science, biology, polymers, soft materials. Endstations: Serial crystallography Diffractive imaging Nanosurveyor...

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    Filter Results Filter by Subject crystal structure (2) design (2) affinity (1) applied life sciences (1) aromatics (1) basic biological sciences (1) biology (1) crystallography (1) ...

  18. Beamline 5.0.3

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    0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION Operational Yes ...

  19. Beamline 5.0.3

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    Beamline 5.0.3 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION ...

  20. PowerPoint Presentation

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    a Protein Crystallography Station (PCS) at the Lujan Neutron Scattering Center for the international structural biology ... housed in a brand new, state- of-the-art laboratory space. ...

  1. Beamline 11.3.1

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    1 Print Small-molecule crystallography Beamline 11.3.1 web site Scientific disciplines: Structural chemistry, magnetic materials, microporous materials. GENERAL BEAMLINE...

  2. Beamline 11.3.1

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    3.1 Print Small-molecule crystallography Beamline 11.3.1 web site Scientific disciplines: Structural chemistry, magnetic materials, microporous materials. GENERAL BEAMLINE...

  3. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a ...

  4. Search for: All records | DOE PAGES

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    Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a ...

  5. Big Data in Reciprocal Space: Sliding Fast Fourier Transforms...

    Office of Scientific and Technical Information (OSTI)

    Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a ...

  6. Beamline 5.0.1

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    Beamline 5.0.1 Print Berkeley Center for Structural Biology (BCSB) Monochromatic protein crystallography Scientific discipline: Structural biology GENERAL BEAMLINE INFORMATION ...

  7. Search for: All records | SciTech Connect

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    (3) serial femtosecond crystallography (2) xfel (2) algorithms (1) analog-to-digital converters (1) atom scattering (1) basic biological sciences xfel (1) bio-inspired...

  8. Intriguing DNA Editor Has a Structural Trigger

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    representing large and small versions, from Streptococcus pyogenes (SpyCas) and Actinomyces naeslundii (AnaCas9) respectively. Using protein crystallography Beamlines 8.2.2...

  9. Search for: All records | SciTech Connect

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    DOEEI USDOE Energy Information Administration (EIA) ... Nevada Environmental Services Nevada Field Office, Las ... Union of Crystallography;online Comparison of Single Event ...

  10. LANSCE | Lujan Center

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    * Julian Chen, new Protein Crystallography Station lead scientist, carving out elite niche: neutron studies of membrane proteins About Us | Contact Us | Jobs | Library |...

  11. SSRLUO 2012 Executive Committee Members | Stanford Synchrotron...

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    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  12. SSRLUO 2011 Executive Committee Members | Stanford Synchrotron...

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    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  13. DOE Laboratories Help Develop Promising New Cancer Fighting Drug...

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    dependent on harnessing the power of X-ray crystallography, and the role of DOE ... structures, we have an atomic road map to rationally optimize our drug candidates." ...

  14. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution ...

  15. Fluorescence-based optimization of human bitter taste receptor...

    Office of Scientific and Technical Information (OSTI)

    Membrane Protein Crystallography Group, Imperial College London, London SW7 2AZ 5 ; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ...

  16. Search for: All records | SciTech Connect

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    ... ; Wang, Andrew H.-J. ; Core Facility for Protein Crystallography, Academia Sinica, ... Oligoribonucleases are essential components of RNA and DNA metabolism and close homologues ...

  17. Search for: All records | SciTech Connect

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    ... studies were initiated at the Protein Crystallography Station (PCS) at Los ... enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease, respectively. ...

  18. Search for: All records | SciTech Connect

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    ... (1) crystallography (1) diphosphine (1) direct energy conversion homogeneous catalysis ... tungsten (1) iron (1) materials science (1) Filter by Author Bullock, R. Morris ...

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    ... Filter Results Filter by Subject crystallography (1) ferromagnetic shape memory alloy (1) heusler alloys (1) magnetic properties (1) materials science copper alloys (1) Filter by ...

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    superconductivity and superfluidity (1) cooling (1) critical temperature (1) crystallography (1) energy storage (1) epitaxy (1) hardening (1) indium complexes (1) interfacial ...

  1. Supercritical carbon dioxide behavior in porous silica aerogel...

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    Resource Type: Journal Article Resource Relation: Journal Name: Journal of Applied Crystallography; Journal Volume: 44; Journal Issue: 1 Research Org: Oak Ridge National Laboratory ...

  2. Search for: All records | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    ... the large extinction (multiple scattering) errors which occur in inorganic X-ray crystallography, and may be applied to nanocrystals. Our results will be used to understand the ...

  3. Scattering from Star Polymers including Excluded Volume Effects...

    Office of Scientific and Technical Information (OSTI)

    GrantContract Number: AC05-00OR22725 Type: Accepted Manuscript Journal Name: Journal of Applied Crystallography Additional Journal Information: Journal Volume: 47; Journal Issue: ...

  4. High-Pressure Tube Trailers and Tanks

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    ... Crystallography Provides Exhaustive Enumeration Describing All Possible Symmetric Macrolattice Cores Appears cubic Actually C3i * Reduced Symmetry * Struts pass each other, avoid ...

  5. Dr. Andrew Russo

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    Disabling a Killer Virus The CAMD Protein Crystallography beamline was used to determine the structure of a protein that the Venezuelan Equine Encephalitis (VEE) virus requires for...

  6. The structure of colloidal suspensions in submicron confinements...

    Office of Scientific and Technical Information (OSTI)

    Resource Relation: Journal Name: Journal of Applied Crystallography; Journal Volume: 47 Research Org: Oak Ridge National Laboratory (ORNL); Center for Nanophase Materials Sciences ...

  7. National synchrotron light source. Activity report, October 1, 1995--September 30, 1996

    SciTech Connect (OSTI)

    Rothman, E.Z.; Hastings, J.B.

    1997-05-01

    The hard work done by the synchrotron radiation community, in collaboration with all those using large-scale central facilities during 1995, paid off in FY 1996 through the DOE`s Presidential Scientific Facilities Initiative. In comparison with the other DOE synchrotron radiation facilities, the National Synchrotron Light Source benefited least in operating budgets because it was unable to increase running time beyond 100%-nevertheless, the number of station hours was maintained. The major thrust at Brookhaven came from a 15% increase in budget which allowed the recruitment of seven staff in the beamlines support group and permitted a step increment in the funding of the extremely long list of upgrades; both to the sources and to the beamlines. During the December 1995 shutdown, the VUV Ring quadrant around U10-U12 was totally reconstructed. New front ends, enabling apertures up to 90 mrad on U10 and U12, were installed. During the year new PRTs were in formation for the infrared beamlines, encouraged by the investment the lab was able to commit from the initiative funds and by awards from the Scientific Facilities Initiative. A new PRT, specifically for small and wide angle x-ray scattering from polymers, will start work on X27C in FY 1997 and existing PRTs on X26C and X9B working on macromolecular crystallography will be joined by new members. Plans to replace aging radio frequency cavities by an improved design, originally a painfully slow six or eight year project, were brought forward so that the first pair of cavities (half of the project for the X-Ray Ring) will now be installed in FY 1997. Current upgrades to 350 mA initially and to 438 mA later in the X-Ray Ring were set aside due to lack of funds for the necessary thermally robust beryllium windows. The Scientific Facilities Initiative allowed purchase of all 34 windows in FY 1996 so that the power upgrade will be achieved in FY 1997.

  8. Search for: All records | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    ... a large family of metal chalcogenophosphates that ... This analysis lays the framework for building image genomes ... While common for organic and macromolecular chemistry, these ...

  9. Paul Adams

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    Division. Dr. Adams' research focuses on the development of new algorithms and methods for structural biology, structural studies of large macromolecular machines, and...

  10. Search for: All records | SciTech Connect

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    aerosol (2) aerosols macromolecular (1) air (1) air-water interface (1) atmospheric ... and carboxylic acid groups from coastal pollution sources. (ii) The organic composition of ...

  11. Complete Safety Training

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    EHS 0470: General Employee Radiation Training (GERT) Special Training Required for Some Users Laser Safety Users working with a Class 3B4 laser EHS 0302 Macromolecular ...

  12. APS Colloquium | Advanced Photon Source

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    of the National Center for Macromolecular Imaging at Baylor College of Medicine, will give a talk entitled "Electron Cryo-Microscopy of Molecular Machines." Bio and Abstract of...

  13. Center for Nanophase Materials Sciences - Summer Newsletter 2010

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    instruments, and foster interaction with users. I work with the Macromolecular Nanomaterial group within the Functional Polymer Architectures theme. My main duty in CNMS is...

  14. Directed Organization of Functional Materials at Inorganic-Macromolecu...

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    Directed Organization of Functional Materials at Inorganic-Macromolecular Interfaces Research The purpose of this project is to develop a quantitative physical picture of...

  15. Frantisek Svec | Center for Gas SeparationsRelevant to Clean...

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    Frantisek Svec Previous Next List svec Formerly: Facility Director, Organic and Macromolecular Synthesis Facility, Lawrence Berkeley National Laboratory Research Interests: Porous...

  16. Footprinting Technique Gives ALS Users New Insights

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    left: Research Scientist Sayan Gupta, Beamline 5.3.1 Scientist Rich Celestre, and BCSB Head Corie Ralston. XFP, a powerful technique for the study of macromolecular structures...

  17. Molecular Foundry

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    Williams Principal Scientific Engineering Associate, Organic and Macromolecular Synthesis TEWilliams@lbl.gov 510.486.6671 Biography Teresa Williams received a BS in Chemistry...

  18. Center for Nanophase Materials Sciences (CNMS) - Themes

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    is home to our synthetic macromolecular capabilities and our complementary efforts in designing functional materials, including those with hybrid molecular architectures, for...

  19. Application to Export Electric Energy OE Docket No. EA-402 Energia...

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    Application to Export Electric Energy OE Docket No. EA-402 Energia Sierra Juarez U.S., LLC Application from ESJ to export electric energy to Mexico. PDF icon EA-402 ESJ (MX).pdf ...

  20. North American Energy Ministers Take Further Action on Energy...

    Office of Environmental Management (EM)

    ... Eduardo Marin Director for Information Mexico-Secretariat of Energy 011 52 55 5000-6244 Email: emarin@energia.gob.mx Anne Womack Kolton Director of Public Affairs U.S. Department ...

  1. Electronic Structure, Phonon Dynamical Properties, and CO2 Capture...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Electronic Structure, Phonon Dynamical Properties, and CO2 Capture Capability of Na2-xMxZrO3 ( MLi ,K): Density-Functional Calculations and Experimental...

  2. EA-336-A ConocoPhillips Company | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-336-A ConocoPhillips Company Order authorizing ConocoPhillips to export electric energy to Mexico. EA-336-A ConocoPhillips (MX).pdf (999.54 KB) More Documents & Publications ...

  3. EA-184-B MORGAN STANLEY CAPITAL GROUP | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    -B MORGAN STANLEY CAPITAL GROUP EA-184-B MORGAN STANLEY CAPITAL GROUP Order authorizing Morgan Stanley Capital Group to export electric energy to Mexico. EA-184-B MSCG MX.pdf ...

  4. EA-48-I El Paso Electric Company | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8-I El Paso Electric Company EA-48-I El Paso Electric Company Order authorizing El Paso Electric Company to export electric energy to Mexico. PDF icon EA-48-I El Paso (MX).pdf More ...

  5. CX-006725: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Whispered Dismantle and Relocation From 58-MX-10CX(s) Applied: B1.31, B3.11Date: 03/19/2010Location(s): Casper, WyomingOffice(s): RMOTC

  6. Application to Export Electric Energy OE Docket No. EA-406 Sempra...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Electric Energy OE Docket No. EA-406 Sempra Generation, LLC Application from Sempra to export electric energy to Mexico. PDF icon EA-406 Sempra Generation (MX).pdf More...

  7. Application to Export Electric Energy OE Docket No. EA-363-A...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    OE Docket No. EA-363-A Noble Americas Gas & Power Corporation Application from NAG&P to export electric energy to Mexico. PDF icon EA-363-A Noble Americas G&P (MX).pdf More...

  8. Application to Export Electric Energy OE Docket No. 382 Glacial...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Notice Volume 76, No. 157 - Aug. 15, 2011 Application from Glacial Energy of Texas to export electric energy to Mexico. Federal Register Notice. PDF icon EA-382 Glacial MX.pdf...

  9. Application to Export Electric Energy OE Docket No. EA-407 Vitol...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Federal Register Notice, Volume 80, No. 42 - March 4, 2015 Application from Vitol to export electric energy to Mexico. Federal Register Notice. PDF icon EA-407 Vitol (MX).pdf...

  10. Application to Export Electric Energy OE Docket No. EA-145-E...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy OE Docket No. EA-145-E Powerex Corporation Application from Powerex Corp to export electric energy to Mexico. PDF icon EA-145-E Powerex Corp MX.pdf More Documents &...

  11. EA-383 Pilot Power Group Inc. | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-383 Pilot Power Group Inc. Order authorizing Pilot Power Group to export electric energy to Mexico. PDF icon EA-383 Pilot Power MX.pdf More Documents & Publications EA-289-B ...

  12. EA-363-A Noble Americas Gas & Power Corporation | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-363-A Noble Americas Gas & Power Corporation Order authorizing NAG&P to export electric energy to Mexico. PDF icon EA-363-A Noble Americas MX.pdf More Documents & Publications ...

  13. EA-106 Arizona Public Service Company | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-106 Arizona Public Service Company Order authorizing Arizona Public Service Company to export electric energy to Mexico. PDF icon EA-106 Arizona Public Service (MX).pdf More ...

  14. EA-289-B INTERCOM ENERGY INC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-289-B INTERCOM ENERGY INC Order authorizing Intercom Energy Inc. to export electric energy to Mexico. PDF icon EA-289-B Intercom MX.pdf More Documents & Publications EA-318-C ...

  15. EA-405 Del Norte Energy LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-405 Del Norte Energy LLC Order authorizing Del Norte to export electric energy to Mexico. PDF icon EA-405 Del Norte Energy (MX).pdf More Documents & Publications Application to ...

  16. EA-402 Energia Sierra Juarez U.S., LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    402 Energia Sierra Juarez U.S., LLC EA-402 Energia Sierra Juarez U.S., LLC Order authorizing ESJ to export electric energy to Mexico. PDF icon EA-402 ESJUS MX.pdf More Documents & ...

  17. EIA3

    U.S. Energy Information Administration (EIA) Indexed Site

    ... WY-Wyoming Countries: AU-Australia CL-Columbia CN-Canada IS-Indonesia MX-Mexico VZ-Venezuela OT-Other (please specify) "RANK OF COAL (D)" ANT-Anthracite BIT-Bituminous ...

  18. ,"U.S. Natural Gas Pipeline Imports From Mexico (MMcf)"

    U.S. Energy Information Administration (EIA) Indexed Site

    ,,"(202) 586-8800",,,"01292016 9:45:31 AM" "Back to Contents","Data 1: U.S. Natural Gas Pipeline Imports From Mexico (MMcf)" "Sourcekey","N9102MX2" "Date","U.S. Natural Gas...

  19. Application to Export Electric Energy OE Docket No. EA-415 Lion...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-415 Lion Shield Energy, LLC Application from Lion Shield Energy to export electric energy to Mexico. PDF icon EA-415 Lion Shield Energy (MX).pdf More Documents & Publications ...

  20. EA-381 E-T Global Energy | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-381 E-T Global Energy Order authorizing E-T Global Energy to export electric energy to Mexico. File EA-381 ET Global MX.docx More Documents & Publications EA-381 E-T Global ...

  1. Appication to Export Electric Energy OE Docket No. EA-390 Global...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-390 Global Pure Energy, LLC Application from Global Pure Energy to export electric energy to Mexico. PDF icon EA-390 Global Pure Energy (MX).pdf More Documents & Publications ...

  2. EA-387 Energia Renovable S.C., LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    7 Energia Renovable S.C., LLC EA-387 Energia Renovable S.C., LLC Order authorizing Energia Renovable to export electric energy to Mexico. PDF icon EA-387 Energia Renovable (MX).pdf ...

  3. DOE/NRC F 740M | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    0M DOENRC F 740M DOENRC Concise Note (Preprinted) DOE F 740-MX (10.4 KB) More Documents & Publications o:informsfixformsnrc740m.wpf DOENRC F 742 PHYSICAL INVENTORY LISTING

  4. Studies Bolster Promise of Topological Insulators

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    by: Z.-H. Pan and T. Valla (Brookhaven National Laboratory); A.V. Fedorov (ALS); D. Gardner, Y.S. Lee, and S. Chu (Massachusetts Institute of Technology); M.-X. Wang, C. Liu,...

  5. EA-318-C AEP Energy Partners, Inc. | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    18-C AEP Energy Partners, Inc. EA-318-C AEP Energy Partners, Inc. Order authorizing AEP-EP to export electric energy to Mexico. EA-318-C AEP EP MX.pdf (1.55 MB) More Documents & ...

  6. National Environmental Policy Act (NEPA) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Congestion Study 11302010--EDF Trading N.A. Export Authorization MX (EA-373) 11... CN (EA-368) 06172010--EDF Trading N.A. Export Authorization CN (EA-367) 06...

  7. EA-206-B Frontera Generation L.P. | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    6-B Frontera Generation L.P. EA-206-B Frontera Generation L.P. Order authorizing Frontera Generation L.P. to export electricity to Mexico. EA-206-B Frontera (MX).pdf (270.81 KB) ...

  8. EA-149 PacifiCorp | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EA-149 PacifiCorp Order authorizing PacifiCorp to export electric energy to Mexico. EA-149 PacifiCorp (MX).pdf (424.52 KB) More Documents & Publications EA-247-D Constellation ...

  9. The calibration of the WISE W1 and W2 Tully-Fisher relation

    SciTech Connect (OSTI)

    Neill, J. D. [California Institute of Technology, 1200 East California Boulevard, MC 278-17, Pasadena, CA 91125 (United States); Seibert, Mark; Scowcroft, Victoria [The Observatories of the Carnegie Institute of Washington, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Tully, R. Brent [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Courtois, Hlne; Sorce, Jenny G. [Institut de Physique Nucleaire, Universit Claude Bernard Lyon I, F-69100 Lyon (France); Jarrett, T. H. [University of Cape Town, Private Bag X3, Rondebosch 7701, Republic of South Africa (South Africa); Masci, Frank J. [Image Processing and Analysis Center (IPAC), California Institute of Technology, 1200 East California Boulevard, MC 100-22, Pasadena, CA 91125 (United States)

    2014-09-10

    In order to explore local large-scale structures and velocity fields, accurate galaxy distance measures are needed. We now extend the well-tested recipe for calibrating the correlation between galaxy rotation rates and luminositiescapable of providing such distance measuresto the all-sky, space-based imaging data from the Wide-field Infrared Survey Explorer (WISE) W1 (3.4 ?m) and W2 (4.6 ?m) filters. We find a correlation of line width to absolute magnitude (known as the Tully-Fisher relation, TFR) of M{sub W1}{sup b,i,k,a}=?20.35?9.56(log?W{sub mx}{sup i}?2.5) (0.54 mag rms) and M{sub W2}{sup b,i,k,a}=?19.76?9.74(log?W{sub mx}{sup i}?2.5) (0.56 mag rms) from 310 galaxies in 13 clusters. We update the I-band TFR using a sample 9% larger than in Tully and Courtois. We derive M{sub I}{sup b,i,k}=?21.34?8.95(log?W{sub mx}{sup i}?2.5) (0.46 mag rms). The WISE TFRs show evidence of curvature. Quadratic fits give M{sub W1}{sup b,i,k,a}=?20.48?8.36(log?W{sub mx}{sup i}?2.5)+3.60(log?W{sub mx}{sup i}?2.5){sup 2} (0.52 mag rms) and M{sub W2}{sup b,i,k,a}=?19.91?8.40(log?W{sub mx}{sup i}?2.5)+4.32(log?W{sub mx}{sup i}?2.5){sup 2} (0.55 mag rms). We apply an I-band WISE color correction to lower the scatter and derive M{sub C{sub W{sub 1}}}=?20.22?9.12(log?W{sub mx}{sup i}?2.5) and M{sub C{sub W{sub 2}}}=?19.63?9.11(log?W{sub mx}{sup i}?2.5) (both 0.46 mag rms). Using our three independent TFRs (W1 curved, W2 curved, and I band), we calibrate the UNION2 Type Ia supernova sample distance scale and derive H {sub 0} = 74.4 1.4(stat) 2.4(sys) km s{sup 1} Mpc{sup 1} with 4% total error.

  10. MEDIA ADVISORY

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    invited to join students in crystallography experiment May 16, 2014 MEDIA ADVISORY Los Alamos High School chemistry students to get hands-on x-ray experience LOS ALAMOS, N.M., May 16, 2014-Some 20 students from Los Alamos High School's advanced-placement chemistry class will get to put their wits and crystal-growing skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research Park. The students will learn about the history and theory of X-ray crystallography in the

  11. Michael Levitt and Computational Biology

    Office of Scientific and Technical Information (OSTI)

    At that time, X-ray crystallography was used to ascertain the location of atoms like hydrogen, carbon and oxygen in larger molecules like proteins or DNA. Researchers then used the ...

  12. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    AlOx Fe, oxidation at the Fe4N AlOx interface creates Fe3O4, leading to negativemore ... heterostructures with well-controlled crystallography and interface structures. ...

  13. A crystallographer keen on showing off the revealing properties...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    record of demystifying materials as varied as DNA and Martian rocks. "Crystallography has the image of an old science. ... crystals can scatter the light waves of x-rays, thereby ...

  14. ALSNews Vol. 320

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    from Spain, Scotland, and the U.S. has utilized ALS Beamline 11.3.1 (small-molecule crystallography) to characterize the design of such "molecular coolers." Read more... ...

  15. CX-013808: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Understanding the Interactions of Seawater Ions with Amidoxime through X-Ray Crystallography - The University of Alabama CX(s) Applied: B3.6Date: 06/25/2015 Location(s): IdahoOffices(s): Nuclear Energy

  16. SSRLUO 2015 Executive Committee Members | Stanford Synchrotron...

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    ... spectroscopy, micro-X-ray fluorescence mapping, X-ray micro-tomography) with bulk ... crystallography as a graduate student by working on problems in DNA structure with Dr. ...

  17. Beamline 11.3.1

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    11.3.1 Print Tuesday, 20 October 2009 09:22 Small-molecule crystallography Beamline 11.3.1 web site Scientific disciplines: Structural chemistry, magnetic materials, microporous...

  18. Femtosecond X-ray protein nanocrystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source (4). ... We mitigate the problem of radiation damage in crystallography by using pulses briefer ...

  19. MEDIA ADVISORY

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    advanced-placement chemistry class will get to put their wits and crystal-growing skills to the test Monday in the Protein Crystallography Station at the Los Alamos Research...

  20. Beamline 9.0.1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    flux (1.9 GeV, 400 mA) 2.8 x 1015 photonss1%BWcentral cone at 457 eV Resolving power (EE) Undulator bandwidth or 1,000 Endstations Serial crystallography Diffractive...

  1. Probing Spatial, Electronic Structures with X-ray Scattering...

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    Wednesday, September 5, 2012 - 10:45am SLAC, Bldg. 137, Room 226 Gang Chen Seminar: Structures at atomic scales are traditionally determined through X-ray crystallography that ...

  2. Gating of the proton-gated ion channel from Gloeobacter violaceus...

    Office of Scientific and Technical Information (OSTI)

    Title: Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography Authors: Gonzalez-Gutierrez, Giovanni ; Cuello, Luis G. ; ...

  3. GCPCC home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Prospective users can contact us via e-mail at hbellamyatlsudotedu or call Henry Bellamy at (225) 578- 9342. We continue to offer mail-in crystallography to both...

  4. LANL

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    MX Factor A Peacekeeper missile being test-launched from Vandenberg Air Force Base, CA. The Peacekeeper, also known as the MX missile (for Missile-eXperimental), was a land-based, intercontinental ballistic missile deployed starting in 1986. The Peacekeeper carried up to 10 re-entry vehicles, each armed with a nuclear warhead. The last of the Peacekeeper missiles was decommissioned in 2005. (Photo: U.S. Air Force.) Test films played a strategic-planning role in the debates of the late 1970s and

  5. NSLS 2007 Activity Report (National Synchrotron Light Source Activity Report 2007)

    SciTech Connect (OSTI)

    Miller ,L.; Nasta, K.

    2008-05-01

    The National Synchrotron Light Source is one of the world's most productive and cost-effective user facilities. With 2,219 individual users, about 100 more than last year, and a record-high 985 publications, 2007 was no exception. In addition to producing an impressive array of science highlights, which are included in this Activity Report, many NSLS users were honored this year for their scientific accomplishments. Throughout the year, there were major strides in the development of the scientific programs by strengthening strategic partnerships with major research resources and with the Center for Functional Nanomaterials (CFN). Of particular note, the Consortium for Materials Properties Research in Earth Sciences (COMPRES) received renewed funding for the next five years through the National Science Foundation. COMPRES operates four high-pressure NSLS beamlines--X17B2, X17B3, X17C, and U2A--and serves the earth science community as well as the rapidly expanding segment of researchers using high-pressure techniques in materials, chemical, and energy-related sciences. A joint appointment was made between the NSLS and Stony Brook University to further enhance interactions with COMPRES. There was major progress on two key beamline projects outlined in the Five-Year Strategic Plan: the X25 beamline upgrade and the construction of the X9 small angle scattering (SAXS) beamline. The X25 overhaul, which began with the installation of the in-vacuum mini-gap undulator (MGU) in January 2006, is now complete. X25 is once again the brightest beamline for macromolecular crystallography at the NSLS, and in tandem with the X29 undulator beamline, it will keep the NSLS at the cutting edge in this important area of research. Upgrade work associated with the new MGU and the front end for the X9 SAXS beamline--jointly developed by the NSLS and the CFN--also was completed. Beamline X9 will host the SAXS program that currently exists at beamline X21 and will provide new microbeam SAXS

  6. LOS ALAMOS, N.M., October 9, 2012-Researchers at Los Alamos National

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    crystallography aids drug design October 9, 2012 Precisely tailored pharmaceuticals could reduce medical side effects LOS ALAMOS, N.M., October 9, 2012-Researchers at Los Alamos National Laboratory have used neutron crystallography for the first time to determine the structure of a clinical drug in complex with its human target enzyme. Seeing the detailed structure of the bonded components provides insights into developing more effective drugs with fewer side effects for patients. The atomic

  7. John Bacik

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    John Bacik John Bacik-Enzyme detective Molecular biology postdoc John Bacik studies enzymes that are key to biofuel production. August 25, 2015 John Bacik John Bacik. "Crystallography is a form of high-resolution microscopy, and our station houses one of the world's premier neutron crystallography instruments." Enzyme detective If Laboratory postdoc John-Paul (John) Bacik gets his wish, the world will significantly reduce its fossil fuel dependence in time for his young daughter's

  8. News Item

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Defining Structure in Synthetic Proteins Predicted 3-dimensional structures, an N-aryl trimer and N-alkyl trimer (top) and a larger cyclic nonamer (bottom) later confirmed by X-ray crystallography results. Scientific Achievement Blind conformational predictions were performed for 3 new peptoids using Replica Exchange Molecular Dynamics simulation and Quantum Mechanical refinement. Subsequent comparison with the 3D structure determined by X-ray crystallography showed these predictions to be

  9. Bioscience

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Bioscience Print Bioscience research at the ALS can be divided into two areas: general biology (microscopy/spectroscopy) and structural biology (crystallography/diffraction). These fields provide complementary approaches to the study of living organisms from the molecular to the cellular levels. Crystallography is used to determine the atomic-resolution, three-dimensional structures of proteins and nucleic acids-the building blocks of life-as well as complexes of these molecules, the

  10. Center for Nanophase Materials Sciences (CNMS) - Functional Polymer...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of non-covalent interactions in the self-assembly of energy-responsive macromolecular systems. Here the focus is on substrate-free (solution-phase) assembly of conjugated...

  11. 99M-Technetium labeled tin colloid radiopharmaceuticals

    DOE Patents [OSTI]

    Winchell, Harry S.; Barak, Morton; Van Fleet, III, Parmer

    1976-07-06

    An improved 99m-technetium labeled tin(II) colloid, size-stabilized for reticuloendothelial organ imaging without the use of macromolecular stabilizers and a packaged tin base reagent and an improved method for making it are disclosed.

  12. SSRLUO 2002 Executive Committee Members | Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Pingitore University of Texas at El Paso Environmental & Geosciences El Paso, TX 79968-0555 Phone: 915-747-5754 Fax: 915-747-5073 E-mail: nick@geo.utep.edu MACROMOLECULAR...

  13. Center for Nanophase Materials Sciences - Summer Newsletter 2010

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in Kingsport, Tennessee as a Research Chemist where I worked in the Specialty Plastics Business. I joined the CNMS in 2007 as part of the Macromolecular Nanomaterials Group and...

  14. RapiData 2015

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Home Announcement Application Schedule Participant Information Vendor Information Location Transportation RapiData 2015 Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement May 3-8, 2015 RapiData 2015 Download Image 1 | Download image 2 RapiData 2015 is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the course is to educate and train young scientists in data

  15. EA-289-C Intercom Energy, Inc. | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    C Intercom Energy, Inc. EA-289-C Intercom Energy, Inc. Order from Intercom Energy to export electric energy Mexico. EA-289-C Intercom Energy MX.pdf (677.97 KB) More Documents & Publications EA-289-B INTERCOM ENERGY INC Application to Export Electric Energy OE Docket No. EA-289-C Intercom Energy, Inc. EA-318-C AEP Energy Partners

  16. EA-378 Cargill Power Markets LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8 Cargill Power Markets LLC EA-378 Cargill Power Markets LLC Order authorizing Cargill Power Markets to export electric energy to Mexico. EA-378 CPM MX.pdf (2.58 MB) More Documents & Publications EA-378-A Cargill Power Markets, LLC EA-384 NRG Power Marketing

  17. EA-378-A Cargill Power Markets, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    -A Cargill Power Markets, LLC EA-378-A Cargill Power Markets, LLC Order authorizing CPM to export electric energy to Mexico. EA-378-A Cargill Power Mkts (MX).pdf (666.68 KB) More Documents & Publications EA-378 Cargill Power Markets LLC EA-209-D Cargill Power Markets, LLC EA-357-A Hunt Electric Power Marketing, L.L.C.

  18. EA-384 NRG Power Marketing LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    4 NRG Power Marketing LLC EA-384 NRG Power Marketing LLC Order authorizing NRG Power Marketing to export electric energy to Mexico. EA-384 NRGPML MX.pdf (767.99 KB) More Documents & Publications Application to Export Electric Energy OE Docket No. EA-384 NRG Power Marketing LLC EA-378 Cargill Power Markets LLC EA-413 Elan Energy Services, LLC

  19. EA-418 Termoelectrica U.S., LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8 Termoelectrica U.S., LLC EA-418 Termoelectrica U.S., LLC Order authorizing Termoelectrica to export electric energy to Mexico. EA-418 Termoelectrica US (MX).pdf (552.92 KB) More Documents & Publications EA-387 Energia Renovable S.C., LLC EA-406 Sempra Generation, LLC EA-357-A Hunt Electric Power Marketing, L.L.C

  20. Large-scale delamination of multi-layers transition metal carbides and carbonitrides “MXenes”

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Naguib, Michael; Unocic, Raymond R.; Armstrong, Beth L.; Nanda, Jagjit

    2015-04-17

    Herein we report on a general approach to delaminate multi-layered MXenes using an organic base to induce swelling that in turn weakens the bonds between the MX layers. Simple agitation or mild sonication of the swollen MXene in water resulted in the large-scale delamination of the MXene layers. The delamination method is demonstrated for vanadium carbide, and titanium carbonitrides MXenes.

  1. Large-Scale Delamination of Multi-Layers Transition Metal Carbides and Carbonitrides MXenes

    SciTech Connect (OSTI)

    Abdelmalak, Michael Naguib; Unocic, Raymond R; Armstrong, Beth L; Nanda, Jagjit

    2015-01-01

    Herein we report on a general approach to delaminate multi-layered MXenes using an organic base to induce swelling that in turn weakens the bonds between the MX layers. Simple agitation or mild sonication of the swollen MXene in water resulted in the large-scale delamination of the MXene layers. The delamination method is demonstrated for vanadium carbide, and titanium carbonitrides MXenes.

  2. Advanced Photon Source Directory | Advanced Photon Source

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    XSD-MPE XSD-MX XSD-OPT XSD-QA XSD-SDM XSD-SPC XSD-SRS XSD-SSM XSD-TRR XSD-XMI Enter the terms you wish to search for. Try this if you're struggling to find the person you are...

  3. FINE-SCALE STRUCTURES OF FLUX ROPES TRACKED BY ERUPTING MATERIAL

    SciTech Connect (OSTI)

    Li Ting; Zhang Jun E-mail: zjun@nao.cas.cn

    2013-06-20

    We present Solar Dynamics Observatory observations of two flux ropes tracked out by material from a surge and a failed filament eruption on 2012 July 29 and August 4, respectively. For the first event, the interaction between the erupting surge and a loop-shaped filament in the east seems to 'peel off' the filament and add bright mass into the flux rope body. The second event is associated with a C-class flare that occurs several minutes before the filament activation. The two flux ropes are, respectively, composed of 85 {+-} 12 and 102 {+-} 15 fine-scale structures, with an average width of about 1.''6. Our observations show that two extreme ends of the flux rope are rooted in opposite polarity fields and each end is composed of multiple footpoints (FPs) of fine-scale structures. The FPs of the fine-scale structures are located at network magnetic fields, with magnetic fluxes from 5.6 Multiplication-Sign 10{sup 18} Mx to 8.6 Multiplication-Sign 10{sup 19} Mx. Moreover, almost half of the FPs show converging motion of smaller magnetic structures over 10 hr before the appearance of the flux rope. By calculating the magnetic fields of the FPs, we deduce that the two flux ropes occupy at least 4.3 Multiplication-Sign 10{sup 20} Mx and 7.6 Multiplication-Sign 10{sup 20} Mx magnetic fluxes, respectively.

  4. Theoretical Studies in Chemical Kinetics - Annual Report, 1970.

    DOE R&D Accomplishments [OSTI]

    Karplus, Martin

    1970-10-01

    The research performed includes (a) Alkali-Halide, Alkali-Halide (MX, M’X’) Exchange Reactions; (b) Inversion Problem; (c) Quantum Mechanics of Scattering Processes, (d) Transition State Analysis of Classical Trajectories, (e) Differential Cross Sections from Classical Trajectories; and (f) Other Studies.

  5. Workbook Contents

    U.S. Energy Information Administration (EIA) Indexed Site

    Cubic Feet)" "Sourcekey","N9132MX3" "Date","Price of U.S. Natural Gas Pipeline Exports to Mexico (Dollars per Thousand Cubic Feet)" 31228,3.99 31593,3.49 31958,3.18 32324,3.21...

  6. Toward Improving the Type IV Cracking Resistance in Cr-Mo Steel Weld Through Thermo-Mechanical Processing

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Shassere, Benjamin A.; Yamamoto, Yukinori; Babu, Sudarsanam Suresh

    2016-02-23

    Detailed microstructure characterization of Grade 91 (Modified 9Cr-1Mo, ASTM A387) steel subjected to a thermo-mechanical treatment (TMT) process was performed to rationalize the cross-weld creep properties. A series of thermo-mechanical processing in the austenite phase region, followed by isothermal aging at temperatures at 973 to 1173 K (700 to 900ºC) was applied to the Grade 91 steel to promote precipitation kinetics of MX (M: Nb and V, X: C and N) in the austenite matrix. Detailed characterization of the base metals after standard tempering confirmed the presence of fine MX dispersion within the tempered martensitic microstructure in steels processed at/andmore » above 1073 K (800 ºC). Relatively low volume fraction of M23C6 precipitates was observed after processing at 1073 K (800 ºC). The cross-weld creep strength after processing was increased with respect to the increase of MX dispersion, indicating that these MX precipitates maintained during weld thermal cycles in the fine grained heat affected zone (FGHAZ) region and thereby contribute to improved creep resistant of welds in comparison to the welds made with the standard “normalization and tempering” processes. Lastly, the steels processed in this specific processing condition showed improved cross-weld creep resistance and sufficient room-temperature toughness. The above data is also analysed based on existing theories of creep deformation based on dislocation climb mechanism.« less

  7. Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery

    SciTech Connect (OSTI)

    Medina, Jesus R.; Blackledge, Charles W.; Heerding, Dirk A.; Campobasso, Nino; Ward, Paris; Briand, Jacques; Wright, Lois; Axten, Jeffrey M.

    2012-05-29

    Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.

  8. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Holistic data analysis and modeling poised to transform protein X-ray crystallography March 29, 2016 Diffuse data integrated in 3-D to reveal dynamics in protein crystals LOS ALAMOS, N.M., March 29, 2016-A new 3-D modeling and data-extraction technique is about to transform the field of X-ray crystallography, with potential benefits for both the pharmaceutical industry and structural biology. A paper this week in Proceedings of the National Academy of Sciences describes the improved blending of

  9. Assembly and Evolution of Complex Fe-S Clusters as Revealed by X-ray

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Crystallography Assembly and Evolution of Complex Fe-S Clusters as Revealed by X-ray Crystallography Complex Fe-S cluster-containing enzymes are ubiquitous in nature where they are involved in a number of fundamental reactions for life including carbon dioxide fixation, nitrogen fixation, and hydrogen metabolism. One of the more complex and unusual biological clusters is found in the [FeFe]-hydrogenase. The active-site H-cluster in these enzymes has a [4Fe-4S] subcluster bridged via a

  10. De-icing: recovery of diffraction intensities in the presence of ice rings

    SciTech Connect (OSTI)

    Chapman, Michael S.; Somasundaram, Thayumanasamy

    2010-11-03

    Macromolecular structures are routinely determined at cryotemperatures using samples flash-cooled in the presence of cryoprotectants. However, sometimes the best diffraction is obtained under conditions where ice formation is not completely ablated, with the result that characteristic ice rings are superimposed on the macromolecular diffraction. In data processing, the reflections that are most affected by the ice rings are usually excluded. Here, an alternative approach of subtracting the ice diffraction is tested. High completeness can be retained with little adverse effect upon the quality of the integrated data. This offers an alternate strategy when high levels of cryoprotectant lead to loss of crystal quality.

  11. Visio-LHCONE VRF 2012-04-30.vsd

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NORDUnet, Copenhagen, Denmark NDGF T1: 109.105.124.0/22 NDGF AS39590 NDGF T1 NORDUNet MX480 NDGF AS39590 NDGF T1 NORDUNet MX480 VRF P2P VRF P2P Amsterdam, Netherlands GEANT LHCONE VRF xxxx ???, 1G V111 10/10G Milan T1600 Paris T1600 Madrid T640 Frankfurt T1600 xxxx DESY Hamb. GSI Darm. KIT Karl. RWTH Aach. xxxx DFN (Germany) DE-KIT, AS 34878: 192.108.45.0/24 192.108.46.0/23 xxxx LHC T1/2/3: xxxx GARR (Italy) CNAF-T1:131.154.128.0/17 INFN Napoli T2: 90.147.67.0/24 V111 10Gbps PIC 6500 V111 1G

  12. Visio-LHCONE VRF 2012-07-02.vsd

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    GARR (Italy) CNAF-T1:131.154.128.0/17 INFN Napoli T2: 90.147.67.0/24 V111 10Gbps PIC 6500 V111 1G GEANT T1600 SARA (Netherlands) NL T1: ASGC M320 1/10G V111 20Gbps 10G to T1 1G -> 10G to T2s Geneva T1600 CERN VRF peering VLAN 111 to GEANT LHCONE VRF CERN VRF peering USLHCNet CoreDirector GEANT Alcatel MCC SURFNet xxxx 10G/10G V111 10/10G NORDUNet MX480 20G shared, NORDUnet 10G shared, NORDUnet to MAN LAN SARA MX960 NIKHEF Deel MLX16 xxxx RENATER (France) GRIF-IN2P3.Orsay: 134.158.72.0/23,

  13. Synergy between Membranes and Microbial Fuel Cells | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Synergy between Membranes and Microbial Fuel Cells Synergy between Membranes and Microbial Fuel Cells Presentation by Jason He, Virginia Tech, during the "Targeting High-Value Challenges" panel at the Hydrogen, Hydrocarbons, and Bioproduct Precursors from Wastewaters Workshop held March 18-19, 2015. Synergy between Membranes and Microbial Fuel Cells (2.52 MB) More Documents & Publications 2011 Alkaline Membrane Fuel Cell Workshop Microbial Fuel Cell Technologies-MxCs: Can They

  14. Ambient-pressure organic superconductor

    DOE Patents [OSTI]

    Williams, Jack M.; Wang, Hsien-Hau; Beno, Mark A.

    1986-01-01

    A new class of organic superconductors having the formula (ET).sub.2 MX.sub.2 wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET).sub.2 AuI.sub.2 exhibits a transition temperature of 5 K which is high for organic superconductors.

  15. Ambient-temperature superconductor symetrical metal-dihalide bis-(ethylenedithio)-tetrathiafulvalene compounds

    DOE Patents [OSTI]

    Williams, Jack M.; Wang, Hsien-Hau; Beno, Mark A.

    1987-01-01

    A new class of organic superconductors having the formula (ET).sub.2 MX.sub.2 wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET).sub.2 AuI.sub.2 exhibits a transition temperature of 5 K. which is high for organic superconductors.

  16. EA-294-B TexMex Energy, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    B TexMex Energy, LLC EA-294-B TexMex Energy, LLC Order authorizing TexMex to export electric energy to Mexico. EA-294-B TexMex MX.pdf (793.38 KB) More Documents & Publications Application to Export Electric Energy OE Docket No. EA-294-B TexMex Energy LLC EA-294-A TexMex Energy, LLC EA-413 Elan Energy Services, LLC

  17. EA-381 E-T Global Energy, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    E-T Global Energy, LLC EA-381 E-T Global Energy, LLC Order authorizing E-T Global to export electric energy to Mexico. EA-381 E-T Global MX.pdf (1.24 MB) More Documents & Publications EA-381 E-T Global Energy Application to export electric energy OE Docket No. EA-381 E-T Global Energy EA-379 FreePoint Commodities

  18. EA-381-A E-T Global Energy, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    -A E-T Global Energy, LLC EA-381-A E-T Global Energy, LLC Order authorizing E-T Global to export electric energy to Mexico. EA-381-A E-T Global (MX).pdf (665.81 KB) More Documents & Publications EA-378-A Cargill Power Markets, LLC EA-387 Energia Renovable S.C., LLC EA-418 Termoelectrica U.S., LLC

  19. EA-413 Elan Energy Services, LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    3 Elan Energy Services, LLC EA-413 Elan Energy Services, LLC Order authorizing Elan Energy to export electric energy to Mexico. EA-413 Elan Energy MX.pdf (975.24 KB) More Documents & Publications Application to Export Electric Energy OE Docket No. EA-413 Elan Energy Services, LLC Application to Export Electric Energy OE Docket No. EA-413 Elan Energy Services, LLC: Federal Register Notice, Volume 80, No. 134 - July 14, 2015 EA-294-B TexMex Energy, LLC

  20. Application to Export Electric Energy OE Docket No. EA-289-C Intercom

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy, Inc.: Federal Register Notice, Volume 81, No. 61 - March 30, 2016 | Department of Energy -C Intercom Energy, Inc.: Federal Register Notice, Volume 81, No. 61 - March 30, 2016 Application to Export Electric Energy OE Docket No. EA-289-C Intercom Energy, Inc.: Federal Register Notice, Volume 81, No. 61 - March 30, 2016 Application from Intercom to export electric energy to Mexico. Federal Register Notice. EA-289-C Intercom Energy MX.pdf (143.05 KB) More Documents & Publications