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

By Alexandre Urzhumtsev, Pavel V. Afonine, Andrew H. Van Benschoten, James Fraser1, Paul D. Adams

1. University of California-San Francisco

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Type

journal-article

Author

Alexandre Urzhumtsev and Pavel V. Afonine and Andrew H. Van Benschoten and James S. Fraser and Paul D. Adams

Citation

Urzhumtsev, A. et al., 2015. From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallogr D, 71(8), pp.1668–1683. Available at: http://dx.doi.org/10.1107/s1399004715011426.

Abstract

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 theT,LandSmatrices 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 theT,LandSmatrix 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 valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of thePHENIXproject.

DOI

Funding

NSF-STC Biology with X-ray Lasers (NSF-1231306)