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 »
- Authors:
-
[2];
[3]
- SLAC National Accelerator Lab., Menlo Park, CA (United States)
- Stanford Univ., Stanford, CA (United States)
- 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. https://doi.org/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. https://doi.org/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 = {Wed Feb 06 00:00:00 EST 2019},
month = {Wed Feb 06 00:00:00 EST 2019}
}
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Table 1: Data statistics. Values in parentheses are for the outer shell.
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