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Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit
The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703569/ https://www.ncbi.nlm.nih.gov/pubmed/19564683 http://dx.doi.org/10.1107/S0907444909010695 |
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author | Ni, Fengyun Poon, Billy K. Wang, Qinghua Ma, Jianpeng |
author_facet | Ni, Fengyun Poon, Billy K. Wang, Qinghua Ma, Jianpeng |
author_sort | Ni, Fengyun |
collection | PubMed |
description | The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed that enables anisotropic B-factor refinement using a drastically smaller number of thermal parameters than even isotropic refinement. Here, the method has been systematically tested on a total of eight systems in the resolution range 3.0–3.9 Å. This series of tests established the most applicable scenarios for the method, the detailed procedures for its application and the degree of structural improvement. The results demonstrated substantial model improvement at the lower resolution limit, especially in cases in which other methods such as the translation–libration–screw (TLS) model were not applicable owing to the poorly converged isotropic B-factor distribution. It is expected that this normal-mode-based method will be a useful tool for structural refinement, in particular at the lower resolution limit, in the field of X-ray crystallography. |
format | Text |
id | pubmed-2703569 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-27035692009-07-01 Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit Ni, Fengyun Poon, Billy K. Wang, Qinghua Ma, Jianpeng Acta Crystallogr D Biol Crystallogr New Algorithms Workshop The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed that enables anisotropic B-factor refinement using a drastically smaller number of thermal parameters than even isotropic refinement. Here, the method has been systematically tested on a total of eight systems in the resolution range 3.0–3.9 Å. This series of tests established the most applicable scenarios for the method, the detailed procedures for its application and the degree of structural improvement. The results demonstrated substantial model improvement at the lower resolution limit, especially in cases in which other methods such as the translation–libration–screw (TLS) model were not applicable owing to the poorly converged isotropic B-factor distribution. It is expected that this normal-mode-based method will be a useful tool for structural refinement, in particular at the lower resolution limit, in the field of X-ray crystallography. International Union of Crystallography 2009-07-01 2009-06-20 /pmc/articles/PMC2703569/ /pubmed/19564683 http://dx.doi.org/10.1107/S0907444909010695 Text en © International Union of Crystallography 2009 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 | New Algorithms Workshop Ni, Fengyun Poon, Billy K. Wang, Qinghua Ma, Jianpeng Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title | Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title_full | Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title_fullStr | Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title_full_unstemmed | Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title_short | Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit |
title_sort | application of normal-mode refinement to x-ray crystal structures at the lower resolution limit |
topic | New Algorithms Workshop |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703569/ https://www.ncbi.nlm.nih.gov/pubmed/19564683 http://dx.doi.org/10.1107/S0907444909010695 |
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