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Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies
Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program w...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243118/ https://www.ncbi.nlm.nih.gov/pubmed/35768542 http://dx.doi.org/10.1038/s42003-022-03575-7 |
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author | De Zitter, Elke Coquelle, Nicolas Oeser, Paula Barends, Thomas R. M. Colletier, Jacques-Philippe |
author_facet | De Zitter, Elke Coquelle, Nicolas Oeser, Paula Barends, Thomas R. M. Colletier, Jacques-Philippe |
author_sort | De Zitter, Elke |
collection | PubMed |
description | Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography. |
format | Online Article Text |
id | pubmed-9243118 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-92431182022-07-01 Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies De Zitter, Elke Coquelle, Nicolas Oeser, Paula Barends, Thomas R. M. Colletier, Jacques-Philippe Commun Biol Article Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography. Nature Publishing Group UK 2022-06-29 /pmc/articles/PMC9243118/ /pubmed/35768542 http://dx.doi.org/10.1038/s42003-022-03575-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article De Zitter, Elke Coquelle, Nicolas Oeser, Paula Barends, Thomas R. M. Colletier, Jacques-Philippe Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title | Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title_full | Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title_fullStr | Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title_full_unstemmed | Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title_short | Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
title_sort | xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243118/ https://www.ncbi.nlm.nih.gov/pubmed/35768542 http://dx.doi.org/10.1038/s42003-022-03575-7 |
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