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Title: Single-particle imaging without symmetry constraints at an X-ray free-electron laser

Abstract

The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1471255
Alternate Identifier(s):
OSTI ID: 1490704
Grant/Contract Number:  
AC02-05CH11231; AC02-76SF00515
Resource Type:
Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Name: IUCrJ Journal Volume: 5 Journal Issue: 6; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 47 OTHER INSTRUMENTATION; single-particle imaging; three-dimensional virus reconstructions; XFELs

Citation Formats

Rose, Max, Bobkov, Sergey, Ayyer, Kartik, Kurta, Ruslan P., Dzhigaev, Dmitry, Kim, Young Yong, Morgan, Andrew J., Yoon, Chun Hong, Westphal, Daniel, Bielecki, Johan, Sellberg, Jonas A., Williams, Garth, Maia, Filipe R. N. C., Yefanov, Olexander M., Ilyin, Vyacheslav, Mancuso, Adrian P., Chapman, Henry N., Hogue, Brenda G., Aquila, Andrew, Barty, Anton, and Vartanyants, Ivan A. Single-particle imaging without symmetry constraints at an X-ray free-electron laser. United Kingdom: N. p., 2018. Web. doi:10.1107/S205225251801120X.
Rose, Max, Bobkov, Sergey, Ayyer, Kartik, Kurta, Ruslan P., Dzhigaev, Dmitry, Kim, Young Yong, Morgan, Andrew J., Yoon, Chun Hong, Westphal, Daniel, Bielecki, Johan, Sellberg, Jonas A., Williams, Garth, Maia, Filipe R. N. C., Yefanov, Olexander M., Ilyin, Vyacheslav, Mancuso, Adrian P., Chapman, Henry N., Hogue, Brenda G., Aquila, Andrew, Barty, Anton, & Vartanyants, Ivan A. Single-particle imaging without symmetry constraints at an X-ray free-electron laser. United Kingdom. doi:10.1107/S205225251801120X.
Rose, Max, Bobkov, Sergey, Ayyer, Kartik, Kurta, Ruslan P., Dzhigaev, Dmitry, Kim, Young Yong, Morgan, Andrew J., Yoon, Chun Hong, Westphal, Daniel, Bielecki, Johan, Sellberg, Jonas A., Williams, Garth, Maia, Filipe R. N. C., Yefanov, Olexander M., Ilyin, Vyacheslav, Mancuso, Adrian P., Chapman, Henry N., Hogue, Brenda G., Aquila, Andrew, Barty, Anton, and Vartanyants, Ivan A. Tue . "Single-particle imaging without symmetry constraints at an X-ray free-electron laser". United Kingdom. doi:10.1107/S205225251801120X.
@article{osti_1471255,
title = {Single-particle imaging without symmetry constraints at an X-ray free-electron laser},
author = {Rose, Max and Bobkov, Sergey and Ayyer, Kartik and Kurta, Ruslan P. and Dzhigaev, Dmitry and Kim, Young Yong and Morgan, Andrew J. and Yoon, Chun Hong and Westphal, Daniel and Bielecki, Johan and Sellberg, Jonas A. and Williams, Garth and Maia, Filipe R. N. C. and Yefanov, Olexander M. and Ilyin, Vyacheslav and Mancuso, Adrian P. and Chapman, Henry N. and Hogue, Brenda G. and Aquila, Andrew and Barty, Anton and Vartanyants, Ivan A.},
abstractNote = {The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.},
doi = {10.1107/S205225251801120X},
journal = {IUCrJ},
number = 6,
volume = 5,
place = {United Kingdom},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1107/S205225251801120X

Citation Metrics:
Cited by: 7 works
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    Works referencing / citing this record:

    Single-particle imaging without symmetry constraints at an X-ray free-electron laser
    dataset, January 2018

    • Rose, Max
    • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); DESY, CFEL, SLAC
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    Single-particle imaging without symmetry constraints at an X-ray free-electron laser
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    • Rose, Max; Bobkov, Sergey; Ayyer, Kartik
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
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