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 Hogue; Andrew Aquila; Anton Barty; Ivan A. Vartanyants

doi:10.1107/S205225251801120X

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 Hogue, Andrew Aquila, Anton BartyIvan A. Vartanyants

Research output: Contribution to journal › Article › peer-review

62 Scopus citations

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 language	English (US)
Pages (from-to)	727-736
Number of pages	10
Journal	IUCrJ
Volume	5
DOIs	https://doi.org/10.1107/S205225251801120X
State	Published - 2018

Keywords

XFELs
single-particle imaging
three-dimensional virus reconstructions

ASJC Scopus subject areas

General Chemistry
Biochemistry
General Materials Science
Condensed Matter Physics

Access to Document

10.1107/S205225251801120X

Cite this

Rose, M., Bobkov, S., Ayyer, K., Kurta, R. P., Dzhigaev, D., Kim, Y. Y., Morgan, A. J., Yoon, C. H., Westphal, D., Bielecki, J., Sellberg, J. A., Williams, G., Maia, F. R. N. C., Yefanov, O. M., Ilyin, V., Mancuso, A. P., Chapman, H. N., Hogue, B., Aquila, A., ... 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, 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, B, 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

@article{2beae288c0974d42916f06f3b6d9daf7,

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.",

keywords = "XFELs, single-particle imaging, three-dimensional virus reconstructions",

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 Brenda Hogue and Andrew Aquila and Anton Barty and Vartanyants, {Ivan A.}",

note = "Publisher Copyright: {\textcopyright} 2018 Max Rose et al.",

year = "2018",

doi = "10.1107/S205225251801120X",

language = "English (US)",

volume = "5",

pages = "727--736",

journal = "IUCrJ",

issn = "2052-2525",

publisher = "International Union of Crystallography",

}

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

AU - Aquila, Andrew

AU - Barty, Anton

AU - Vartanyants, Ivan A.

PY - 2018

Y1 - 2018

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.

KW - XFELs

KW - single-particle imaging

KW - three-dimensional virus reconstructions

UR - http://www.scopus.com/inward/record.url?scp=85056165262&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85056165262&partnerID=8YFLogxK

U2 - 10.1107/S205225251801120X

DO - 10.1107/S205225251801120X

M3 - Article

AN - SCOPUS:85056165262

SN - 2052-2525

VL - 5

SP - 727

EP - 736

JO - IUCrJ

JF - IUCrJ

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this