Asymmetry in serial femtosecond crystallography data
Abstract
Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of theBlastochloris viridisphotosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Braggmore »
- Authors:
-
[1]
- Univ. of Gothenburg (Sweden). Dept. of Chemistry and Molecular Biology
- Univ. of Gothenburg (Sweden). Dept. of Chemistry and Molecular Biology; Univ. of Southern California, Los Angeles, CA (United States). Dept. of Chemistry, Bridge Inst.
- Publication Date:
- Research Org.:
- Stanford Linear Accelerator Center (SLAC), CA (United States). Linac Coherent Light Source (LCLS)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1625836
- Grant/Contract Number:
- AC02-76SF00515
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section A, Foundations and Advances (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section A, Foundations and Advances (Online); Journal Volume: 73; Journal Issue: 2; Journal ID: ISSN 2053-2733
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Chemistry; Crystallography; ex-Gaussian distribution; serial femtosecond crystallography; Bragg reflections; systematic absences; intensity distribution
Citation Formats
Sharma, Amit, Johansson, Linda, Dunevall, Elin, Wahlgren, Weixiao Y., Neutze, Richard, and Katona, Gergely. Asymmetry in serial femtosecond crystallography data. United States: N. p., 2017.
Web. doi:10.1107/s2053273316018696.
Sharma, Amit, Johansson, Linda, Dunevall, Elin, Wahlgren, Weixiao Y., Neutze, Richard, & Katona, Gergely. Asymmetry in serial femtosecond crystallography data. United States. https://doi.org/10.1107/s2053273316018696
Sharma, Amit, Johansson, Linda, Dunevall, Elin, Wahlgren, Weixiao Y., Neutze, Richard, and Katona, Gergely. Mon .
"Asymmetry in serial femtosecond crystallography data". United States. https://doi.org/10.1107/s2053273316018696. https://www.osti.gov/servlets/purl/1625836.
@article{osti_1625836,
title = {Asymmetry in serial femtosecond crystallography data},
author = {Sharma, Amit and Johansson, Linda and Dunevall, Elin and Wahlgren, Weixiao Y. and Neutze, Richard and Katona, Gergely},
abstractNote = {Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of theBlastochloris viridisphotosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.},
doi = {10.1107/s2053273316018696},
journal = {Acta Crystallographica. Section A, Foundations and Advances (Online)},
number = 2,
volume = 73,
place = {United States},
year = {Mon Jan 30 00:00:00 EST 2017},
month = {Mon Jan 30 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
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:
An alternative method for data analysis in serial femtosecond crystallography
journal, October 2014
- Zhang, Tao; Li, Yang; Wu, Lijie
- Acta Crystallographica Section A Foundations and Advances, Vol. 70, Issue 6
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
Lipidic Sponge Phase Crystal Structure of a Photosynthetic Reaction Center Reveals Lipids on the Protein Surface
journal, October 2009
- Wöhri, Annemarie B.; Wahlgren, Weixiao Y.; Malmerberg, Erik
- Biochemistry, Vol. 48, Issue 41
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
journal, July 2015
- Kang, Yanyong; Zhou, X. Edward; Gao, Xiang
- Nature, Vol. 523, Issue 7562
De novo protein crystal structure determination from X-ray free-electron laser data
journal, November 2013
- Barends, Thomas R. M.; Foucar, Lutz; Botha, Sabine
- Nature, Vol. 505, Issue 7482
First lasing and operation of an ångstrom-wavelength free-electron laser
journal, August 2010
- Emma, P.; Akre, R.; Arthur, J.
- Nature Photonics, Vol. 4, Issue 9
How to use MATLAB to fit the ex-Gaussian and other probability functions to a distribution of response times
journal, March 2008
- Lacouture, Yves; Cousineau, Denis
- Tutorials in Quantitative Methods for Psychology, Vol. 4, Issue 1
Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography
journal, December 2013
- Johansson, Linda C.; Arnlund, David; Katona, Gergely
- Nature Communications, Vol. 4, Issue 1
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
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
journal, May 2012
- Boutet, S.; Lomb, L.; Williams, G. J.
- Science, Vol. 337, Issue 6092
Femtosecond protein nanocrystallography—data analysis methods
journal, January 2010
- Kirian, Richard A.; Wang, Xiaoyu; Weierstall, Uwe
- Optics Express, Vol. 18, Issue 6
Femtosecond X-ray protein nanocrystallography
journal, February 2011
- Chapman, Henry N.; Fromme, Petra; Barty, Anton
- Nature, Vol. 470, Issue 7332, p. 73-77
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Estimating the difference between structure-factor amplitudes using multivariate Bayesian inference
journal, March 2016
- Katona, Gergely; Garcia-Bonete, Maria-José; Lundholm, Ida V.
- Acta Crystallographica Section A Foundations and Advances, Vol. 72, Issue 3
On the treatment of negative intensity observations
journal, July 1978
- French, S.; Wilson, K.
- Acta Crystallographica Section A, Vol. 34, Issue 4
Lipidic phase membrane protein serial femtosecond crystallography
journal, January 2012
- Johansson, Linda C.; Arnlund, David; White, Thomas A.
- Nature Methods, Vol. 9, Issue 3
Lipidic cubic phase serial millisecond crystallography using synchrotron radiation
journal, March 2015
- Nogly, Przemyslaw; James, Daniel; Wang, Dingjie
- IUCrJ, Vol. 2, Issue 2, p. 168-176
Serial femtosecond crystallography: the first five years
journal, February 2015
- Schlichting, Ilme
- IUCrJ, Vol. 2, Issue 2, p. 246-255
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
Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein
journal, December 2014
- Tenboer, Jason; Basu, Shibom; Zatsepin, Nadia
- Science, Vol. 346, Issue 6214
A profile refinement method for nuclear and magnetic structures
journal, June 1969
- Rietveld, H. M.
- Journal of Applied Crystallography, Vol. 2, Issue 2, p. 65-71
Femtosecond diffractive imaging with a soft-X-ray free-electron laser
journal, November 2006
- Chapman, Henry N.; Barty, Anton; Bogan, Michael J.
- Nature Physics, Vol. 2, Issue 12
Probabilistic programming in Python using PyMC3
journal, January 2016
- Salvatier, John; Wiecki, Thomas V.; Fonnesbeck, Christopher
- PeerJ Computer Science, Vol. 2
Potential for biomolecular imaging with femtosecond X-ray pulses
journal, August 2000
- Neutze, Richard; Wouts, Remco; van der Spoel, David
- Nature, Vol. 406, Issue 6797
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Equation of State Calculations by Fast Computing Machines
journal, June 1953
- Metropolis, Nicholas; Rosenbluth, Arianna W.; Rosenbluth, Marshall N.
- The Journal of Chemical Physics, Vol. 21, Issue 6
Indexing in single-crystal diffractometry with an obstinate list of reflections
journal, April 1992
- Duisenberg, A. J. M.
- Journal of Applied Crystallography, Vol. 25, Issue 2
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
The integration of macromolecular diffraction data
journal, December 2005
- Leslie, Andrew G. W.
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1
Works referencing / citing this record:
A practical guide to developing virtual and augmented reality exercises for teaching structural biology: VR and AR for Teaching Structural Biology
journal, November 2018
- Garcia-Bonete, Maria-Jose; Jensen, Maja; Katona, Gergely
- Biochemistry and Molecular Biology Education, Vol. 47, Issue 1