Detection of internal cavities in globular proteins.

We have undertaken a study of internal cavities in five protein structure groups, each containing different crystallographic structure determinations of the same protein, to understand better the nature of packing defects in protein tertiary architectures. Our results show that cavity detection and consistency of detection are highly dependent on probe and cavity size, cavity position within the globular protein and the local "quality' (r.m.s. deviation) of structural consistency within the group. The consistency of solvent placement within cavities has also been examined. We provide guidelines for estimating the likelihood of a given cavity to be an actual packing defect or to be a result of experimental error.