DEVIATIONS FROM STANDARD ATOMIC VOLUMES AS A QUALITY MEASURE FOR PROTEIN CRYSTAL-STRUCTURES

Standard ranges of atomic and residue volumes are computed in 64 highl y resolved and well-refined protein crystal structures using the class ical Voronoi procedure. Deviations of the atomic volumes from the stan dard values, evaluated as the volume Z-scores, are used to assess the quality of protein crystal structures. To score a structure globally, we compute the volume Z-score root mean square deviation (2-score rms) , which measures the average magnitude of the volume irregularities in the structure. We find that the Z-score rms decreases as the resoluti on and R-factor improve, consistent with the fact that these improveme nts generally reflect more accurate models. From the Z-score rms distr ibution in structures with a given resolution or X-factor, we determin e the normal limits in Z-score rms values for structures solved at tha t resolution or X-factor. Structures whose Z-score rms exceeds these l imits are considered as outliers. Such structures also exhibit unusual stereochemistry, as revealed by other analyses. Absolute Z-scores of individual atoms are used to identify problems in specific regions wit hin a protein model. These Z-scores correlate fairly well with the ato mic B-factors, and atoms having absolute Z-scores >3, occur at or near regions in the model where programs such as PROCHECK identify unusual stereochemistry. Atomic volumes, themselves not directly restrained i n crystallographic refinement, can thus provide an independent, rather sensitive, measure of the quality of a protein structure. The volume- based structure validation procedures are implemented in the program P ROVE (PROtein Volume Evaluation), which is accessible through the Worl d Wide Web. (C) 1996 Academic Press Limited