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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2020
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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. |
format | Online Article Text |
id | pubmed-7642788 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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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