Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Beyond integration: modeling every pixel to obtain better structure factors from stills

Abstract

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (104-106) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb3+L-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter ofmore » each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.« less

Authors:
 [1];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1];  [2];  [1]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Univ. of California, San Francisco, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division; National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1764541
Alternate Identifier(s):
OSTI ID: 1779684
Grant/Contract Number:  
AC02-05CH11231; GM117126; AC02-76SF00515; GM124149; GM124169; GM103393; AI150476; GM110501; GM126289; 17-SC-20-SC
Resource Type:
Accepted Manuscript
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 7; Journal Issue: 6; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; serial crystallography; free-electron lasers; SFX; stills; data processing

Citation Formats

Mendez, Derek, Bolotovsky, Robert, Bhowmick, Asmit, Brewster, Aaron S., Kern, Jan, Yano, Junko, Holton, James M., and Sauter, Nicholas K. Beyond integration: modeling every pixel to obtain better structure factors from stills. United States: N. p., 2020. Web. doi:10.1107/s2052252520013007.
Copy to clipboard
Mendez, Derek, Bolotovsky, Robert, Bhowmick, Asmit, Brewster, Aaron S., Kern, Jan, Yano, Junko, Holton, James M., & Sauter, Nicholas K. Beyond integration: modeling every pixel to obtain better structure factors from stills. United States. https://doi.org/10.1107/s2052252520013007
Copy to clipboard
Mendez, Derek, Bolotovsky, Robert, Bhowmick, Asmit, Brewster, Aaron S., Kern, Jan, Yano, Junko, Holton, James M., and Sauter, Nicholas K. Sat . "Beyond integration: modeling every pixel to obtain better structure factors from stills". United States. https://doi.org/10.1107/s2052252520013007. https://www.osti.gov/servlets/purl/1764541.
Copy to clipboard
@article{osti_1764541,
title = {Beyond integration: modeling every pixel to obtain better structure factors from stills},
author = {Mendez, Derek and Bolotovsky, Robert and Bhowmick, Asmit and Brewster, Aaron S. and Kern, Jan and Yano, Junko and Holton, James M. and Sauter, Nicholas K.},
abstractNote = {Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (104-106) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb3+L-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.},
doi = {10.1107/s2052252520013007},
journal = {IUCrJ},
number = 6,
volume = 7,
place = {United States},
year = {Sat Oct 24 00:00:00 EDT 2020},
month = {Sat Oct 24 00:00:00 EDT 2020}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1107/s2052252520013007
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Polarization correction for crystal-monochromatized X-radiation
journal, November 1955

CrystFEL : a software suite for snapshot serial crystallography
journal, March 2012

  • White, Thomas A.; Kirian, Richard A.; Martin, Andrew V.
  • Journal of Applied Crystallography, Vol. 45, Issue 2
  • DOI: 10.1107/S0021889812002312

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures
journal, September 2014

  • Holton, James M.; Classen, Scott; Frankel, Kenneth A.
  • The FEBS Journal, Vol. 281, Issue 18
  • DOI: 10.1111/febs.12922

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism
journal, May 2020

  • Ibrahim, Mohamed; Fransson, Thomas; Chatterjee, Ruchira
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 23
  • DOI: 10.1073/pnas.2000529117

On the limited memory BFGS method for large scale optimization
journal, August 1989

  • Liu, Dong C.; Nocedal, Jorge
  • Mathematical Programming, Vol. 45, Issue 1-3
  • DOI: 10.1007/BF01589116

Experimental phasing of serial femtosecond crystallography data
journal, September 2017

A simplified description of X-ray free-electron lasers
journal, January 2011

Two-colour hard X-ray free-electron laser with wide tunability
journal, December 2013

  • Hara, Toru; Inubushi, Yuichi; Katayama, Tetsuo
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3919

ChipX: A Novel Microfluidic Chip for Counter-Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature
journal, July 2013

  • Pinker, Franziska; Brun, Mathieu; Morin, Pierre
  • Crystal Growth & Design, Vol. 13, Issue 8
  • DOI: 10.1021/cg301757g

Accurate determination of segmented X-ray detector geometry
journal, January 2015

  • Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius
  • Optics Express, Vol. 23, Issue 22
  • DOI: 10.1364/OE.23.028459

Application of an ePix100 detector for coherent scattering using a hard X-ray free-electron laser
journal, August 2016

  • Sikorski, Marcin; Feng, Yiping; Song, Sanghoon
  • Journal of Synchrotron Radiation, Vol. 23, Issue 5
  • DOI: 10.1107/S1600577516010869

The high-mosaicity illusion: revealing the true physical characteristics of macromolecular crystals
journal, August 2000

  • Bellamy, Henry D.; Snell, Edward H.; Lovelace, Jeff
  • Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 8
  • DOI: 10.1107/S0907444900007356

New Python-based methods for data processing
journal, June 2013

  • Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000863

DIALS : implementation and evaluation of a new integration package
journal, February 2018

  • Winter, Graeme; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2
  • DOI: 10.1107/S2059798317017235

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing
journal, March 2016

  • Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 3
  • DOI: 10.1107/S2059798315019269

Femtosecond protein nanocrystallography—data analysis methods
journal, January 2010

  • Kirian, Richard A.; Wang, Xiaoyu; Weierstall, Uwe
  • Optics Express, Vol. 18, Issue 6
  • DOI: 10.1364/OE.18.005713

Femtosecond X-ray protein nanocrystallography
journal, February 2011

  • Chapman, Henry N.; Fromme, Petra; Barty, Anton
  • Nature, Vol. 470, Issue 7332, p. 73-77
  • DOI: 10.1038/nature09750

Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source
journal, July 2018

A single-shot transmissive spectrometer for hard x-ray free electron lasers
journal, July 2012

  • Zhu, Diling; Cammarata, Marco; Feldkamp, Jan M.
  • Applied Physics Letters, Vol. 101, Issue 3
  • DOI: 10.1063/1.4736725

The point-spread function of fiber-coupled area detectors
journal, September 2012

  • Holton, James M.; Nielsen, Chris; Frankel, Kenneth A.
  • Journal of Synchrotron Radiation, Vol. 19, Issue 6
  • DOI: 10.1107/S0909049512035571

SwissFEL: The Swiss X-ray Free Electron Laser
journal, July 2017

  • Milne, Christopher; Schietinger, Thomas; Aiba, Masamitsu
  • Applied Sciences, Vol. 7, Issue 7
  • DOI: 10.3390/app7070720

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

A Description of Imperfections in Protein Crystals
journal, September 1998

Improved crystal orientation and physical properties from single-shot XFEL stills
journal, November 2014

  • Sauter, Nicholas K.; Hattne, Johan; Brewster, Aaron S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 12
  • DOI: 10.1107/S1399004714024134

XCII. The reflexion of X-rays from imperfect crystals
journal, May 1922

  • Darwin, C. G.
  • The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, Vol. 43, Issue 257
  • DOI: 10.1080/14786442208633940

Small-angle scattering and the structure of ambient liquid water
journal, July 2010

  • Clark, G. N. I.; Hura, G. L.; Teixeira, J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 32
  • DOI: 10.1073/pnas.1006599107

Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs
journal, January 2016

  • Alonso-Mori, R.; Asa, K.; Bergmann, U.
  • Faraday Discussions, Vol. 194
  • DOI: 10.1039/C6FD00084C

An Approach to Distribution of the Product of Two Normal Variables
journal, January 2012

  • Oliveira, Amilcar; Seijas-Macias, Antonio
  • Discussiones Mathematicae Probability and Statistics, Vol. 32, Issue 1-2
  • DOI: 10.7151/dmps.1146

Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies
journal, December 2019

  • Nango, Eriko; Kubo, Minoru; Tono, Kensuke
  • Applied Sciences, Vol. 9, Issue 24
  • DOI: 10.3390/app9245505

Asymmetry in serial femtosecond crystallography data
journal, January 2017

  • Sharma, Amit; Johansson, Linda; Dunevall, Elin
  • Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue 2
  • DOI: 10.1107/S2053273316018696

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction
journal, August 2017

  • Thomaston, Jessica L.; Woldeyes, Rahel A.; Nakane, Takanori
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 51
  • DOI: 10.1073/pnas.1705624114

Accounting for partiality in serial crystallography using ray-tracing principles
journal, August 2015

  • Kroon-Batenburg, Loes M. J.; Schreurs, Antoine M. M.; Ravelli, Raimond B. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 9
  • DOI: 10.1107/S1399004715011803

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source
journal, October 2004

  • MacDowell, Alastair A.; Celestre, Rich S.; Howells, Malcolm
  • Journal of Synchrotron Radiation, Vol. 11, Issue 6
  • DOI: 10.1107/S0909049504024835

Femtosecond and Subfemtosecond X-Ray Pulses from a Self-Amplified Spontaneous-Emission–Based Free-Electron Laser
journal, February 2004

Demonstration of Single-Crystal Self-Seeded Two-Color X-Ray Free-Electron Lasers
journal, December 2014

Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction
journal, June 1982

Post-refinement method for snapshot serial crystallography
journal, July 2014

  • White, Thomas A.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
  • DOI: 10.1098/rstb.2013.0330

Recent developments in CrystFEL
journal, March 2016

  • White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang
  • Journal of Applied Crystallography, Vol. 49, Issue 2
  • DOI: 10.1107/S1600576716004751

Whole-pattern fitting technique in serial femtosecond nanocrystallography
journal, February 2016

A convolutional neural network-based screening tool for X-ray serial crystallography
journal, April 2018

  • Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.
  • Journal of Synchrotron Radiation, Vol. 25, Issue 3, p. 655-670
  • DOI: 10.1107/S1600577518004873

An intensity evaluation method: EVAL -14
journal, March 2003

  • Duisenberg, Albert J. M.; Kroon-Batenburg, Loes M. J.; Schreurs, Antoine M. M.
  • Journal of Applied Crystallography, Vol. 36, Issue 2
  • DOI: 10.1107/S0021889802022628

Development of a hard X-ray split-and-delay line and performance simulations for two-color pump-probe experiments at the European XFEL
journal, June 2018

  • Lu, W.; Friedrich, B.; Noll, T.
  • Review of Scientific Instruments, Vol. 89, Issue 6
  • DOI: 10.1063/1.5027071

An Algorithm for Automatic Indexing of Oscillation Images using Fourier Analysis
journal, December 1997

  • Steller, I.; Bolotovsky, R.; Rossmann, M. G.
  • Journal of Applied Crystallography, Vol. 30, Issue 6
  • DOI: 10.1107/S0021889897008777

On the release of cppxfel for processing X-ray free-electron laser images
journal, May 2016

  • Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.
  • Journal of Applied Crystallography, Vol. 49, Issue 3
  • DOI: 10.1107/S1600576716006981

pinkIndexer – a universal indexer for pink-beam X-ray and electron diffraction snapshots
journal, January 2020

  • Gevorkov, Yaroslav; Barty, Anton; Brehm, Wolfgang
  • Acta Crystallographica Section A Foundations and Advances, Vol. 76, Issue 2
  • DOI: 10.1107/S2053273319015559

Processing of X-ray snapshots from crystals in random orientations
journal, July 2014

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 8
  • DOI: 10.1107/S1399004714013534

Structural basis of cell-cell adhesion by cadherins
journal, March 1995

  • Shapiro, Lawrence; Fannon, Allison M.; Kwong, Peter D.
  • Nature, Vol. 374, Issue 6520
  • DOI: 10.1038/374327a0

X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
journal, July 1993

  • Henke, B. L.; Gullikson, E. M.; Davis, J. C.
  • Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342
  • DOI: 10.1006/adnd.1993.1013

Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex
journal, October 2016

  • Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Zeldin, Oliver B.
  • eLife, Vol. 5
  • DOI: 10.7554/eLife.18740

Matching X-ray beam and detector properties to protein crystals of different perfection
journal, March 2014

Improving signal strength in serial crystallography with DIALS geometry refinement
journal, September 2018

  • Brewster, Aaron S.; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 9
  • DOI: 10.1107/S2059798318009191

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography
journal, November 2016

  • Stagno, J. R.; Liu, Y.; Bhandari, Y. R.
  • Nature, Vol. 541, Issue 7636
  • DOI: 10.1038/nature20599

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser
journal, June 2018

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction
journal, February 2020

  • Sauter, Nicholas K.; Kern, Jan; Yano, Junko
  • Acta Crystallographica Section D Structural Biology, Vol. 76, Issue 2
  • DOI: 10.1107/S2059798320000418

The CSPAD megapixel x-ray camera at LCLS
conference, October 2012

  • Hart, Philip; Boutet, Sébastien; Carini, Gabriella
  • SPIE Optical Engineering + Applications, SPIE Proceedings
  • DOI: 10.1117/12.930924

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein
journal, May 2016

XFEL diffraction: developing processing methods to optimize data quality
journal, January 2015

AGIPD, a high dynamic range fast detector for the European XFEL
journal, January 2015

Using a non-monochromatic microbeam for serial snapshot crystallography
journal, April 2013

  • Dejoie, Catherine; McCusker, Lynne B.; Baerlocher, Christian
  • Journal of Applied Crystallography, Vol. 46, Issue 3
  • DOI: 10.1107/S0021889813005888

The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002

  • Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
  • Journal of Applied Crystallography, Vol. 35, Issue 1
  • DOI: 10.1107/S0021889801017824

Implementing the Nelder-Mead simplex algorithm with adaptive parameters
journal, May 2010

EVAL15 : a diffraction data integration method based on ab initio predicted profiles
journal, December 2009

  • Schreurs, Antoine M. M.; Xian, Xinyi; Kroon-Batenburg, Loes M. J.
  • Journal of Applied Crystallography, Vol. 43, Issue 1
  • DOI: 10.1107/S0021889809043234

SAD phasing of XFEL data depends critically on the error model
journal, October 2019

  • Brewster, Aaron S.; Bhowmick, Asmit; Bolotovsky, Robert
  • Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 11
  • DOI: 10.1107/S2059798319012877

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis
journal, December 2019

  • Dasgupta, Medhanjali; Budday, Dominik; de Oliveira, Saulo H. P.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 51
  • DOI: 10.1073/pnas.1901864116

Reconstruction algorithm for single-particle diffraction imaging experiments
journal, August 2009

X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser
journal, April 2018

Integration of macromolecular diffraction data
journal, October 1999

  • Leslie, A. G. W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 10
  • DOI: 10.1107/S090744499900846X

The minimum crystal size needed for a complete diffraction data set
journal, March 2010

  • Holton, James M.; Frankel, Kenneth A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007262

Diffraction before destruction
journal, July 2014

  • Chapman, Henry N.; Caleman, Carl; Timneanu, Nicusor
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
  • DOI: 10.1098/rstb.2013.0313

XFELs for structure and dynamics in biology
journal, May 2017

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
journal, March 2015

  • Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.
  • eLife, Vol. 4
  • DOI: 10.7554/eLife.05421

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate
journal, November 2017

  • Tosha, Takehiko; Nomura, Takashi; Nishida, Takuma
  • Nature Communications, Vol. 8, Article No. 1585
  • DOI: 10.1038/s41467-017-01702-1

Angle calculations for 3- and 4-circle X-ray and neutron diffractometers
journal, April 1967

Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008

  • DePonte, D. P.; Weierstall, U.; Schmidt, K.
  • Journal of Physics D: Applied Physics, Vol. 41, Issue 19, Article No. 195505
  • DOI: 10.1088/0022-3727/41/19/195505

Structures of the intermediates of Kok’s photosynthetic water oxidation clock
journal, November 2018

Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector
journal, October 2018

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: