On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures

Correlation coefficients (CCs) between the mean atomic displacement parameters (B values) of the main-chain and the side-chain atoms in selected high-resolution protein structures are distributed over a broad range (0.5–1.0). The distribution of CCs is found to be related to the mean difference in B values of C^α and C^β atoms. High CCs are also associated with the frequent occurrence of consecutive C^α atoms with relatively high B values. The distribution of CCs and its relation to the mean difference between the B values of C^α and C^β atoms shows dependence on the package used for refinement (X-PLOR, PROLSQ or TNT). These observations reflect the differences in the way B-value constraints are handled in these packages. Further differences are discernible in the distributions for proteins refined using the same package. It is likely that these differences are related to the different refinement protocols or weighting schemes followed by investigators. The resolution of these issues is important for evolving correct strategies for the refinement of the atomic displacement parameters in X-ray diffraction studies of proteins. Furthermore, it may be possible to develop refinement-validation tools by observing the features that are invariant in the distribution of atomic displacement parameters.