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Macromolecular refinement by model morphing using non-atomic parameterizations

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution...

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Autores principales: Cowtan, Kevin, Agirre, Jon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947776/
https://www.ncbi.nlm.nih.gov/pubmed/29533238
http://dx.doi.org/10.1107/S205979831701350X
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author Cowtan, Kevin
Agirre, Jon
author_facet Cowtan, Kevin
Agirre, Jon
author_sort Cowtan, Kevin
collection PubMed
description Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.
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spelling pubmed-59477762018-05-15 Macromolecular refinement by model morphing using non-atomic parameterizations Cowtan, Kevin Agirre, Jon Acta Crystallogr D Struct Biol Research Papers Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model. International Union of Crystallography 2018-02-01 /pmc/articles/PMC5947776/ /pubmed/29533238 http://dx.doi.org/10.1107/S205979831701350X Text en © Cowtan & Agirre 2018 http://creativecommons.org/licenses/by/2.0/uk/ 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/2.0/uk/
spellingShingle Research Papers
Cowtan, Kevin
Agirre, Jon
Macromolecular refinement by model morphing using non-atomic parameterizations
title Macromolecular refinement by model morphing using non-atomic parameterizations
title_full Macromolecular refinement by model morphing using non-atomic parameterizations
title_fullStr Macromolecular refinement by model morphing using non-atomic parameterizations
title_full_unstemmed Macromolecular refinement by model morphing using non-atomic parameterizations
title_short Macromolecular refinement by model morphing using non-atomic parameterizations
title_sort macromolecular refinement by model morphing using non-atomic parameterizations
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947776/
https://www.ncbi.nlm.nih.gov/pubmed/29533238
http://dx.doi.org/10.1107/S205979831701350X
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