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Title: From deep TLS validation to ensembles of atomic models built from elemental motions

Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of validmore » underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less
Authors:
 [1] ;  [2] ;  [3] ; ;  [4] ;  [3] ;  [5] ;  [2]
  1. Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)
  2. (France)
  3. Lawrence Berkeley National Laboratory, Berkeley, California (United States)
  4. University of California, San Francisco, San Francisco, CA 94158 (United States)
  5. (United States)
Publication Date:
OSTI Identifier:
22389078
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 8; Other Information: PMCID: PMC4528800; PMID: 26249348; PUBLISHER-ID: rr5096; OAI: oai:pubmedcentral.nih.gov:4528800; Copyright (c) Urzhumtsev et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; DECOMPOSITION; DIFFUSE SCATTERING; MATRIX ELEMENTS; S MATRIX; VALIDATION; VISIBLE RADIATION