Agreement Factors Crystallography

Here, we study the impact of mediatization by many structurally different conformers in a protein crystal on isotropic and anisotropic B factors obtained in crystallographic refining with more modern simulation and refining approaches. In particular, we analyze a system in which, unlike a typical crystallographic experiment, microscopic variability is perfectly controlled and manipulated directly. Specifically, we use MD simulations to create a microscopic model of a Villin head crystallizing domain with prefabricated structural heterogeneity. Villin Hairstyle is a 35-protein residue 3-Helix and is one of the most studied model systems in protein biophysics due to its small size and rapid foldable properties. We generate extensive crystal simulations with 216 explicitly modeled molecules, in which all contributions to B factors other than thermal atomic movements have been eliminated. In particular, we achieve great structural diversity through 350K MD simulations, but we maintain 60% of the atoms of each molecule fixed by position constraints, limiting their dynamics while eliminating the movements of the protein`s star bodies. The remaining 40% of atoms in each molecule are free to explore different conformations. Then we calculate the structural factors for the simulated crystal, the average, and then solve the structure by molecular replacement (MR) and various refining processes. Finally, we analyze the resulting model and compare refined isotropic or isotropic factors B with their MD-based counterparties, which in turn represent actual atomic variations in the system used to produce structural factors. Such an internal self-resistant comparison between the refined model and the known microscopic set of the simulation allows us to examine how X-ray acidification can detect the true structural diversity of a biomolecule at the microscopic level.