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. 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...

  16. 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 ...

  17. 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....

  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. 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 ...

  20. 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 ...

  1. 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 ...

  2. 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...

  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. 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, ...

  17. 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

  18. 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 ...

  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. 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.

  7. 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. ; ...

  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. 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

  14. 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.

  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. 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 ...

  17. 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

  18. 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.

  19. 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.

  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. 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 ...

  12. JBLULCE

    Energy Science and Technology Software Center (OSTI)

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

  13. 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

  14. 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.

  15. 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.

  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. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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

  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. 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:...

  20. 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...

  1. 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 ...

  2. 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...

  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

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  10. EA-338_Shell_Energy_MX.pdf

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  11. EA-341_Photovoltaic_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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  19. EA-387 Energia Renovable (MX).pdf

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  20. EA-401 Lonestar (MX).pdf

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  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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  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

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    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)

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

  17. 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...

  18. --No Title--

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    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...

  19. 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...

  20. 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, ...

  1. 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...

  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. 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...

  5. 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 ...

  6. 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...

  7. 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 ...

  8. 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 ...

  9. 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.;

  10. 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 ...

  11. PP-304_GDD_-_WAPA__San_Luis_MX.pdf

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  12. 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 ...

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

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    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

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  9. 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...

  10. 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 ...

  11. 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.

  12. EA-149 PacifiCorp (MX).pdf

    Office of Environmental Management (EM)

  13. 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

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

    Office of Environmental Management (EM)

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

    Office of Environmental Management (EM)

  16. 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...

  17. 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...

  18. 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.

  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

    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

  2. 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.

  3. 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

  4. 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 ...

  5. 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

  6. 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,...

  7. 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

  8. 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, ...

  9. 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 ; ...

  10. 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