Dataset Information

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

ABSTRACT: Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16?807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

SUBMITTER: Joosten RP

PROVIDER: S-EPMC3246819 | biostudies-other | 2009 Jun

REPOSITORIES: biostudies-other

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Publications

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Joosten Robbie P RP Salzemann Jean J Bloch Vincent V Stockinger Heinz H Berglund Ann-Charlott AC Blanchet Christophe C Bongcam-Rudloff Erik E Combet Christophe C Da Costa Ana L AL Deleage Gilbert G Diarena Matteo M Fabbretti Roberto R Fettahi Géraldine G Flegel Volker V Gisel Andreas A Kasam Vinod V Kervinen Timo T Korpelainen Eija E Mattila Kimmo K Pagni Marco M Reichstadt Matthieu M Breton Vincent V Tickle Ian J IJ Vriend Gert G

Journal of applied crystallography 20090403 Pt 3

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X ...[more]

PMID: 22477769

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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

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Publications

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Similar Datasets

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