skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns

Abstract

Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm–Diederichs algorithm [Brehm & Diederichs (2014[Brehm, W. & Diederichs, K. (2014). Acta Cryst. D70, 101-109.]), Acta Cryst. D70, 101–109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE–complexin-1–synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFELmore » diffraction data sets.« less

Authors:
 [1];  [1]; ORCiD logo [2];  [2]; ORCiD logo [3]
  1. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  2. Stanford Univ., Stanford, CA (United States)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1507027
Grant/Contract Number:  
AC02-76SF00515; AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 75; Journal Issue: 2; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; serial crystallography; indexing ambiguity; XFELs

Citation Formats

Uervirojnangkoorn, Monarin, Lyubimov, Artem Y., Zhou, Qiangjun, Weis, William I., and Brunger, Axel T. Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns. United States: N. p., 2019. Web. doi:10.1107/s2059798318013177.
Uervirojnangkoorn, Monarin, Lyubimov, Artem Y., Zhou, Qiangjun, Weis, William I., & Brunger, Axel T. Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns. United States. doi:10.1107/s2059798318013177.
Uervirojnangkoorn, Monarin, Lyubimov, Artem Y., Zhou, Qiangjun, Weis, William I., and Brunger, Axel T. Wed . "Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns". United States. doi:10.1107/s2059798318013177. https://www.osti.gov/servlets/purl/1507027.
@article{osti_1507027,
title = {Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns},
author = {Uervirojnangkoorn, Monarin and Lyubimov, Artem Y. and Zhou, Qiangjun and Weis, William I. and Brunger, Axel T.},
abstractNote = {Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm–Diederichs algorithm [Brehm & Diederichs (2014[Brehm, W. & Diederichs, K. (2014). Acta Cryst. D70, 101-109.]), Acta Cryst. D70, 101–109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE–complexin-1–synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.},
doi = {10.1107/s2059798318013177},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 2,
volume = 75,
place = {United States},
year = {2019},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Table 1 Table 1: Data statistics.

Values in parentheses are for the outer shell.


Save / Share:

Works referenced in this record:

Goniometer-based femtosecond crystallography with X-ray free electron lasers
journal, October 2014

  • Cohen, Aina E.; Soltis, S. Michael; González, Ana
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 48, p. 17122-17127
  • DOI: 10.1073/pnas.1418733111

The primed SNARE–complexin–synaptotagmin complex for neuronal exocytosis
journal, August 2017

  • Zhou, Qiangjun; Zhou, Peng; Wang, Austin L.
  • Nature, Vol. 548, Issue 7668
  • DOI: 10.1038/nature23484

Breaking the indexing ambiguity in serial crystallography
journal, December 2013

  • Brehm, Wolfgang; Diederichs, Kay
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 1
  • DOI: 10.1107/S1399004713025431

Collective instabilities and high-gain regime in a free electron laser
journal, July 1984


Processing and post-refinement of oscillation camera data
journal, December 1979

  • Rossmann, M. G.; Leslie, A. G. W.; Abdel-Meguid, S. S.
  • Journal of Applied Crystallography, Vol. 12, Issue 6
  • DOI: 10.1107/S0021889879013273

Surprises and pitfalls arising from (pseudo)symmetry
journal, December 2007

  • Zwart, Peter H.; Grosse-Kunstleve, Ralf W.; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705531X

Scaling and assessment of data quality
journal, December 2005

  • Evans, Philip
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
  • DOI: 10.1107/S0907444905036693

IOTA : integration optimization, triage and analysis tool for the processing of XFEL diffraction images
journal, May 2016

  • Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Zeldin, Oliver B.
  • Journal of Applied Crystallography, Vol. 49, Issue 3
  • DOI: 10.1107/S1600576716006683

The derivation of the axes of the conventional unit cell from the dimensions of the Buerger-reduced cell
journal, June 1982


A revised partiality model and post-refinement algorithm for X-ray free-electron laser data
journal, May 2015

  • Ginn, Helen Mary; Brewster, Aaron S.; Hattne, Johan
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 6
  • DOI: 10.1107/S1399004715006902

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

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

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

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

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

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

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

The oscillation method for crystals with very large unit cells
journal, November 1979

  • Winkler, F. K.; Schutt, C. E.; Harrison, S. C.
  • Acta Crystallographica Section A, Vol. 35, Issue 6
  • DOI: 10.1107/S0567739479002035

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
  • DOI: 10.1107/S0907444909052925

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
journal, March 2014

  • Hattne, Johan; Echols, Nathaniel; Tran, Rosalie
  • Nature Methods, Vol. 11, Issue 5
  • DOI: 10.1038/nmeth.2887

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.