The key differences in protein x-ray crystal and solution NMR structures

The ability to determine the structure of a protein to near-atomic resolution using x-ray crystallography and NMR spectroscopy has been vital for advances in structural biology. However, it is unclear whether or not the structures obtained from these two methods are the same to within experimental uncertainties, or if these characterization methods influence the structures in some way. To address this important question, we compiled a dataset of paired high-resolution x-ray crystal structures and high-quality NMR structures to determine whether there are any systematic differences between the structures solved using the two experimental techniques. Backbone fluctuations of core C_α atoms reveal that core residues from x-ray crystal structures occupy smaller regions of configuration space than core residues in NMR structures. We also find that the core residues of NMR structures are more densely packed than core residues in x-ray crystal structures. We explain this result by preparing packings of amino-acid-shaped particles with thermalized packing-generation protocols, and find that packings with higher thermalization resemble cores in NMR structures, while in the limit of no thermalization we recover packings that resemble the cores of x-ray crystal structures. This result suggests that the differences between NMR and x-ray crystal structures are caused by the varying degree of thermal fluctuations in the two characterization methods. NMR solution structures are allowed to fluctuate more, which compacts the core, but allows for greater exploration of core configurations. In contrast, x-ray crystal structures occupy only well-defined, smaller regions of configuration space.