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Title: Protein crystal structure from non-oriented, single-axis sparse X-ray data

Abstract

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotronmore » radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases where the data are sparse.« less

Authors:
 [1];  [2];  [2];  [2];  [2];  [3]
  1. Cornell Univ., Ithaca, NY (United States). Biophysics Field; Cornell Univ., Ithaca, NY (United States). Cornell High Energy Synchrotron Source (CHESS)
  2. Cornell Univ., Ithaca, NY (United States). Lab. of Atomic and Solid State Physics
  3. Cornell Univ., Ithaca, NY (United States). Cornell High Energy Synchrotron Source (CHESS); Cornell Univ., Ithaca, NY (United States). Lab. of Atomic and Solid State Physics
Publication Date:
Research Org.:
Cornell Univ., Ithaca, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1393427
Grant/Contract Number:  
FG02-10ER46693; SC0004079
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; X-ray serial microcrystallography; sparse data; EMC algorithm; protein microcrystallography; synchrotron-radiation sources

Citation Formats

Wierman, Jennifer L., Lan, Ti-Yen, Tate, Mark W., Philipp, Hugh T., Elser, Veit, and Gruner, Sol M. Protein crystal structure from non-oriented, single-axis sparse X-ray data. United States: N. p., 2016. Web. doi:10.1107/S2052252515018795.
Wierman, Jennifer L., Lan, Ti-Yen, Tate, Mark W., Philipp, Hugh T., Elser, Veit, & Gruner, Sol M. Protein crystal structure from non-oriented, single-axis sparse X-ray data. United States. doi:10.1107/S2052252515018795.
Wierman, Jennifer L., Lan, Ti-Yen, Tate, Mark W., Philipp, Hugh T., Elser, Veit, and Gruner, Sol M. Fri . "Protein crystal structure from non-oriented, single-axis sparse X-ray data". United States. doi:10.1107/S2052252515018795. https://www.osti.gov/servlets/purl/1393427.
@article{osti_1393427,
title = {Protein crystal structure from non-oriented, single-axis sparse X-ray data},
author = {Wierman, Jennifer L. and Lan, Ti-Yen and Tate, Mark W. and Philipp, Hugh T. and Elser, Veit and Gruner, Sol M.},
abstractNote = {X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases where the data are sparse.},
doi = {10.1107/S2052252515018795},
journal = {IUCrJ},
number = 1,
volume = 3,
place = {United States},
year = {Fri Jan 01 00:00:00 EST 2016},
month = {Fri Jan 01 00:00:00 EST 2016}
}

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Works referenced in this record:

Room-temperature macromolecular serial crystallography using synchrotron radiation
journal, May 2014


Lipidic cubic phase serial millisecond crystallography using synchrotron radiation
journal, March 2015


Integration, scaling, space-group assignment and post-refinement
journal, January 2010

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