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

Max Rose, Sergey Bobkov, Kartik Ayyer, Ruslan P. Kurta, Dmitry Dzhigaev, Young Yong Kim, Andrew J. Morgan, Chun Hong Yoon, Daniel Westphal, Johan Bielecki, Jonas A. Sellberg, Garth Williams, Filipe R.N.C. Maia, Olexander M. Yefanov, Vyacheslav Ilyin, Adrian P. Mancuso, Henry N. Chapman, Brenda G. Hogue, Andrew Aquila, Anton Barty & 1 others Ivan A. Vartanyants

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)727-736
Number of pages10
JournalIUCrJ
Volume5
DOIs
Publication statusPublished - 2018 Jan 1

Fingerprint

X ray lasers
Free electron lasers
viruses
Viruses
free electron lasers
Lasers
X-Rays
Electrons
Imaging techniques
symmetry
bacteriophages
Bacteriophages
x rays
Workflow
Diffraction patterns
Carrier concentration
indication
diffraction patterns
Diffraction
Experiments

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry
  • Materials Science(all)
  • Condensed Matter Physics

Cite this

Rose, M., Bobkov, S., Ayyer, K., Kurta, R. P., Dzhigaev, D., Kim, Y. Y., ... Vartanyants, I. A. (2018). Single-particle imaging without symmetry constraints at an X-ray free-electron laser. IUCrJ, 5, 727-736. https://doi.org/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. In: IUCrJ. 2018 ; Vol. 5. pp. 727-736.
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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.",
author = "Max Rose and Sergey Bobkov and Kartik Ayyer and Kurta, {Ruslan P.} and Dmitry Dzhigaev and Kim, {Young Yong} and Morgan, {Andrew J.} and Yoon, {Chun Hong} and Daniel Westphal and Johan Bielecki and Sellberg, {Jonas A.} and Garth Williams and Maia, {Filipe R.N.C.} and Yefanov, {Olexander M.} and Vyacheslav Ilyin and Mancuso, {Adrian P.} and Chapman, {Henry N.} and Hogue, {Brenda G.} and Andrew Aquila and Anton Barty and Vartanyants, {Ivan A.}",
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Rose, M, Bobkov, S, Ayyer, K, Kurta, RP, Dzhigaev, D, Kim, YY, Morgan, AJ, Yoon, CH, Westphal, D, Bielecki, J, Sellberg, JA, Williams, G, Maia, FRNC, Yefanov, OM, Ilyin, V, Mancuso, AP, Chapman, HN, Hogue, BG, Aquila, A, Barty, A & Vartanyants, IA 2018, 'Single-particle imaging without symmetry constraints at an X-ray free-electron laser', IUCrJ, vol. 5, pp. 727-736. https://doi.org/10.1107/S205225251801120X

Single-particle imaging without symmetry constraints at an X-ray free-electron laser. / 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.

In: IUCrJ, Vol. 5, 01.01.2018, p. 727-736.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Single-particle imaging without symmetry constraints at an X-ray free-electron laser

AU - Rose, Max

AU - Bobkov, Sergey

AU - Ayyer, Kartik

AU - Kurta, Ruslan P.

AU - Dzhigaev, Dmitry

AU - Kim, Young Yong

AU - Morgan, Andrew J.

AU - Yoon, Chun Hong

AU - Westphal, Daniel

AU - Bielecki, Johan

AU - Sellberg, Jonas A.

AU - Williams, Garth

AU - Maia, Filipe R.N.C.

AU - Yefanov, Olexander M.

AU - Ilyin, Vyacheslav

AU - Mancuso, Adrian P.

AU - Chapman, Henry N.

AU - Hogue, Brenda G.

AU - Aquila, Andrew

AU - Barty, Anton

AU - Vartanyants, Ivan A.

PY - 2018/1/1

Y1 - 2018/1/1

N2 - 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.

AB - 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.

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DO - 10.1107/S205225251801120X

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JO - IUCrJ

JF - IUCrJ

SN - 2052-2525

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