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Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

Abstract：

:A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In this model, the atomic fluctuations are treated as anisotropic and concerted. The normal modes of the external motion (TLS model) are also introduced to cover the factors other than the internal fluctuations, such as the lattice disorder and diffusion. A program for the normal mode refinement (NM-REF) has been developed. The method has first been tested against simulated diffraction data for human lysozyme calculated by a Monte Carlo simulation. Applications of the method have demonstrated that the normal mode refinement has: (1) improved the fitting to the diffraction data, even with fewer adjustable parameters; (2) distinguished internal fluctuations from external ones; (3) determined anisotropic thermal factors; and (4) identified concerted fluctuations in the protein molecule.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Kidera A,Go N

doi

10.1016/0022-2836(92)90932-a

keywords:

subject

Has Abstract

pub_date

1992-05-20 00:00:00

pages

457-75

issue

2

eissn

0022-2836

issn

1089-8638

pii

0022-2836(92)90932-A

journal_volume

225

pub_type

杂志文章

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