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Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

ABSTRACT: 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 A. 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.

SUBMITTER: Ni F

PROVIDER: S-EPMC2703569 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

Ni Fengyun F Poon Billy K BK Wang Qinghua Q Ma Jianpeng J

Acta crystallographica. Section D, Biological crystallography 20090620 Pt 7

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 eigh ...[more]

PMID: 19564683

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Project description:This study aims to solve the site-occupancy issues of any crystalline substance, showing that the structure refinement results should not be limited to a simple description of the crystal geometry but should go beyond that, providing refined site-scattering values consistent with the chemical data. A detailed description of the structure of the amphibole-supergroup minerals is very challenging owing to their complex chemical composition that renders the process of cation partition extremely difficult, particularly because of the occurrence of multivalent elements. Since amphiboles naturally occur under a fibrous morphology and have largely been used to produce asbestos, there is a growing demand for detailed and accurate structural data in order to study the relationships between structure, composition and toxicity. The present study proposes a recommended refinement procedure for both X-ray single-crystal structure refinement (SREF) and Rietveld analysis for tremolite, selected as a test case. The corresponding structural results are compared to estimate the ‘degree of confidence’ of the Rietveld refinement with regard to SREF. In particular, it is shown that the interpretation of the electron density of the tremolite structure by SREF is model dependent. By assuming that the site-scattering values from SREF should be as close as possible to those from electron microprobe analysis, as a crucial constraint for the correct description of the final crystal-chemical model, it is found that it is best satisfied by using partially ionized scattering curves (SCs) for O and Si, and neutral SCs (neutral oxygen curves or NOCs) for other atoms. This combination leads to the best fit to the diffraction data. Moreover, it is found that Rietveld refinement using NOCs produces the best structural results, in excellent agreement with SREF. It is worth noting that, due to the complexity of the diffraction pattern and the fairly large number of freely refinable parameters, refinements with different combinations of SCs produce results almost indistinguishable from a statistical point of view, albeit showing significant differences from a structural point of view.

Dataset Information

Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

Publications

Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

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