Expanding the model: anisotropic displacement parameters in protein structure refinement

Recent technological improvements in crystallographic data collection have led to a surge in the number of protein structures being determined at atom ic or near-atomic resolution. At this resolution, structural models can be expanded to include anisotropic displacement parameters (ADPs) for individu al atoms. New protocols and new tools are needed to refine, analyze and val idate such models optimally. One such tool, PARVATI, has been used to exami ne all protein structures (peptide chains >50 residues) for which expanded models including ADPs are available from the Protein Data Bank. The distrib ution of anisotropy within each of these refined models is broadly similar across the entire set of structures, with a mean anisotropy A in the range 0.4-0.5, This is a significant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and R-free. The observed distribution of aniso tropy may prove useful in the validation of very high resolution structures . A more complete understanding of this distribution may also allow the dev elopment of improved protein structural models, even at lower resolution.