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Using more than 801?296 small-molecule crystal structures to aid in protein structure refinement and analysis.

ABSTRACT: The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement.

SUBMITTER: Cole JC

PROVIDER: S-EPMC5349435 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis.

Cole Jason C JC Giangreco Ilenia I Groom Colin R CR

Acta crystallographica. Section D, Structural biology 20170222 Pt 3

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical ...[more]

PMID: 28291758

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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

Using more than 801?296 small-molecule crystal structures to aid in protein structure refinement and analysis.

Publications

Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis.

Similar Datasets

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