Data from: Modelling dynamics in protein crystal structures by ensemble refinement

Single-structure models derived from X-ray data do not adequately account
for the inherent, functionally important dynamics of protein molecules. We
generated ensembles of structures by time-averaged refinement, where local
molecular vibrations were sampled by molecular-dynamics (MD) simulation
whilst global disorder was partitioned into an underlying overall
translation–libration–screw (TLS) model. Modeling of 20 protein datasets
at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%,
indicating that ensemble models fit the X-ray data better than single
structures. The ensembles revealed that, while most proteins display a
well-ordered core, some proteins exhibit a ‘molten core’ likely supporting
functionally important dynamics in ligand binding, enzyme activity and
protomer assembly. Order–disorder changes in HIV protease indicate a
mechanism of entropy compensation for ordering the catalytic residues upon
ligand binding by disordering specific core residues. Thus, ensemble
refinement extracts dynamical details from the X-ray data that allow a
more comprehensive understanding of structure–dynamics–function
relationships.