Evaluation of Molecular Perturbation of a Deuterated Protein by Temperature Factor Refinement in X-Ray Structural Analysis of High-Resolution Diffraction Data

Structural analysis of deuterated proteins, which are essential for neutron protein crystallography, involves refinement of X-ray crystallographic data using atomic or molecular thermal stability factors. Analysis of high resolution (~0.9 Å) X-ray data can localize some of the hydrogen atoms in a protein molecule. Thermal stabilities and temperature factors are affected by some reasons; one of them is the masses of hydrogen and deuterium atoms. We propose a method to refine X-ray data, taking into account these effects, to show existence probability for deuterium in the protein. Thermal factors were calculated using several physical parameters, and the resultant values were fitted to the experimental thermal factors with high accuracy. This computational method can be applied to analyze and predict the hydrogen/deuterium exchanged states of protein crystals, even small crystals that are unsuitable for neutron crystallography.