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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be cr...

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Autores principales: Terwilliger, Thomas C., Grosse-Kunstleve, Ralf W., Afonine, Pavel V., Adams, Paul D., Moriarty, Nigel W., Zwart, Peter, Read, Randy J., Turk, Dusan, Hung, Li-Wei
Formato: Texto
Lenguaje:English
Publicado: International Union of Crystallography 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483474/
https://www.ncbi.nlm.nih.gov/pubmed/17452785
http://dx.doi.org/10.1107/S0907444907009791
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author Terwilliger, Thomas C.
Grosse-Kunstleve, Ralf W.
Afonine, Pavel V.
Adams, Paul D.
Moriarty, Nigel W.
Zwart, Peter
Read, Randy J.
Turk, Dusan
Hung, Li-Wei
author_facet Terwilliger, Thomas C.
Grosse-Kunstleve, Ralf W.
Afonine, Pavel V.
Adams, Paul D.
Moriarty, Nigel W.
Zwart, Peter
Read, Randy J.
Turk, Dusan
Hung, Li-Wei
author_sort Terwilliger, Thomas C.
collection PubMed
description Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ‘perfect’ structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.
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spelling pubmed-24834742009-03-05 Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models Terwilliger, Thomas C. Grosse-Kunstleve, Ralf W. Afonine, Pavel V. Adams, Paul D. Moriarty, Nigel W. Zwart, Peter Read, Randy J. Turk, Dusan Hung, Li-Wei Acta Crystallogr D Biol Crystallogr Research Papers Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ‘perfect’ structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models. International Union of Crystallography 2007-05-01 2007-04-21 /pmc/articles/PMC2483474/ /pubmed/17452785 http://dx.doi.org/10.1107/S0907444907009791 Text en © International Union of Crystallography 2007 http://journals.iucr.org/services/termsofuse.html This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.
spellingShingle Research Papers
Terwilliger, Thomas C.
Grosse-Kunstleve, Ralf W.
Afonine, Pavel V.
Adams, Paul D.
Moriarty, Nigel W.
Zwart, Peter
Read, Randy J.
Turk, Dusan
Hung, Li-Wei
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title_full Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title_fullStr Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title_full_unstemmed Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title_short Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
title_sort interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483474/
https://www.ncbi.nlm.nih.gov/pubmed/17452785
http://dx.doi.org/10.1107/S0907444907009791
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