MatchMaps: Non-isomorphous difference maps for X-ray crystallography

Conformational change mediates the biological functions of proteins. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands, and time. The isomorphous difference map remains the gold standard for detecting structural differences between datasets. Isomorphous difference maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even minute changes in unit cell dimensions can render isomorphous difference maps useless. This is unnecessary. Here we describe a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. We have implemented this procedure in an open-source python package, MatchMaps, that can be run in any software environment supporting PHENIX and CCP4. Through examples, we show that MatchMaps “rescues” observed difference electron density maps for near-isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit, or across altogether different crystal forms.