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An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Exist...

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Autores principales: Assalauova, Dameli, Kim, Young Yong, Bobkov, Sergey, Khubbutdinov, Ruslan, Rose, Max, Alvarez, Roberto, Andreasson, Jakob, Balaur, Eugeniu, Contreras, Alice, DeMirci, Hasan, Gelisio, Luca, Hajdu, Janos, Hunter, Mark S., Kurta, Ruslan P., Li, Haoyuan, McFadden, Matthew, Nazari, Reza, Schwander, Peter, Teslyuk, Anton, Walter, Peter, Xavier, P. Lourdu, Yoon, Chun Hong, Zaare, Sahba, Ilyin, Viacheslav A., Kirian, Richard A., Hogue, Brenda G., Aquila, Andrew, Vartanyants, Ivan A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642788/
https://www.ncbi.nlm.nih.gov/pubmed/33209321
http://dx.doi.org/10.1107/S2052252520012798
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author Assalauova, Dameli
Kim, Young Yong
Bobkov, Sergey
Khubbutdinov, Ruslan
Rose, Max
Alvarez, Roberto
Andreasson, Jakob
Balaur, Eugeniu
Contreras, Alice
DeMirci, Hasan
Gelisio, Luca
Hajdu, Janos
Hunter, Mark S.
Kurta, Ruslan P.
Li, Haoyuan
McFadden, Matthew
Nazari, Reza
Schwander, Peter
Teslyuk, Anton
Walter, Peter
Xavier, P. Lourdu
Yoon, Chun Hong
Zaare, Sahba
Ilyin, Viacheslav A.
Kirian, Richard A.
Hogue, Brenda G.
Aquila, Andrew
Vartanyants, Ivan A.
author_facet Assalauova, Dameli
Kim, Young Yong
Bobkov, Sergey
Khubbutdinov, Ruslan
Rose, Max
Alvarez, Roberto
Andreasson, Jakob
Balaur, Eugeniu
Contreras, Alice
DeMirci, Hasan
Gelisio, Luca
Hajdu, Janos
Hunter, Mark S.
Kurta, Ruslan P.
Li, Haoyuan
McFadden, Matthew
Nazari, Reza
Schwander, Peter
Teslyuk, Anton
Walter, Peter
Xavier, P. Lourdu
Yoon, Chun Hong
Zaare, Sahba
Ilyin, Viacheslav A.
Kirian, Richard A.
Hogue, Brenda G.
Aquila, Andrew
Vartanyants, Ivan A.
author_sort Assalauova, Dameli
collection PubMed
description An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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spelling pubmed-76427882020-11-17 An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser Assalauova, Dameli Kim, Young Yong Bobkov, Sergey Khubbutdinov, Ruslan Rose, Max Alvarez, Roberto Andreasson, Jakob Balaur, Eugeniu Contreras, Alice DeMirci, Hasan Gelisio, Luca Hajdu, Janos Hunter, Mark S. Kurta, Ruslan P. Li, Haoyuan McFadden, Matthew Nazari, Reza Schwander, Peter Teslyuk, Anton Walter, Peter Xavier, P. Lourdu Yoon, Chun Hong Zaare, Sahba Ilyin, Viacheslav A. Kirian, Richard A. Hogue, Brenda G. Aquila, Andrew Vartanyants, Ivan A. IUCrJ Research Papers An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits. International Union of Crystallography 2020-10-15 /pmc/articles/PMC7642788/ /pubmed/33209321 http://dx.doi.org/10.1107/S2052252520012798 Text en © Assalauova et al. 2020 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Research Papers
Assalauova, Dameli
Kim, Young Yong
Bobkov, Sergey
Khubbutdinov, Ruslan
Rose, Max
Alvarez, Roberto
Andreasson, Jakob
Balaur, Eugeniu
Contreras, Alice
DeMirci, Hasan
Gelisio, Luca
Hajdu, Janos
Hunter, Mark S.
Kurta, Ruslan P.
Li, Haoyuan
McFadden, Matthew
Nazari, Reza
Schwander, Peter
Teslyuk, Anton
Walter, Peter
Xavier, P. Lourdu
Yoon, Chun Hong
Zaare, Sahba
Ilyin, Viacheslav A.
Kirian, Richard A.
Hogue, Brenda G.
Aquila, Andrew
Vartanyants, Ivan A.
An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title_full An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title_fullStr An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title_full_unstemmed An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title_short An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
title_sort advanced workflow for single-particle imaging with the limited data at an x-ray free-electron laser
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642788/
https://www.ncbi.nlm.nih.gov/pubmed/33209321
http://dx.doi.org/10.1107/S2052252520012798
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