Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670

Center for Eukaryotic Structural Genomics (CESG)

Ensemble refinement of protein crystal structures: validation and application.

AUTHOR USED THE SF DATA FROM ENTRY 1YDW. UNMODELED DENSITY APPEARS IN BOTH SUBUNITS IN THE REGION BETWEEN LYS 43 TYR 63 PROBABLY DUE TO NADP.

Center for Eukaryotic Structural Genomics

Original refinement based on same data and R-free set.

This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ydw and the first data set in the deposited structure factor file for 1ydw along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.

Ensemble Refinement, Refinement Methodology Development, AT4G09670, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, OXIDOREDUCTASE