Displacement-Parameter Weighted Coordinate Comparison: I. Detection of Significant Structural Differences Between Oxidation States

A method, displacement-parameter weighted coordinate comparison, for comparing closely related structures is developed. A 'probability of similarity' is derived from the overlap between the most probable volumes occupied by two analogous atoms in a comparison. The distribution of distances between atom pairs (difference distances), where each distance is weighted by the probability of similarity, is examined. The subset of atom pairs with normally distributed difference distances is used to estimate errors in the difference distances and to calculate the probability that the difference is significant for each atom-pair. These probabilities of difference are shown to correlate with features observed in difference maps for diffraction data from oxidized and reduced forms of the cupredoxin, pseudoazurin. The pair-wise probability of difference also is shown to be correlated with regions in previously published plastocyanin structures which differ upon copper oxidation state change, and which differ in a similar manner when temperature is changed, or pH is changed.