Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: De Zitter, Elke, Coquelle, Nicolas, Oeser, Paula, Barends, Thomas R. M., Colletier, Jacques-Philippe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
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
_version_ 1784738233489293312
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
work_keys_str_mv AT dezitterelke xtrapol8enablesautomaticelucidationoflowoccupancyintermediatestatesincrystallographicstudies
AT coquellenicolas xtrapol8enablesautomaticelucidationoflowoccupancyintermediatestatesincrystallographicstudies
AT oeserpaula xtrapol8enablesautomaticelucidationoflowoccupancyintermediatestatesincrystallographicstudies
AT barendsthomasrm xtrapol8enablesautomaticelucidationoflowoccupancyintermediatestatesincrystallographicstudies
AT colletierjacquesphilippe xtrapol8enablesautomaticelucidationoflowoccupancyintermediatestatesincrystallographicstudies