Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Abstract

Using synchrotron radiation, diffraction data extending to 0.70 Å resolution were collected from crystals of the small protein crambin at room temperature (297 K), and the structure was refined with spherical-atom approximation to an R factor of 0.0591, revealing (i) protein regions with multiple conformations, (ii) extended water networks correlated with protein conformations and (iii) minimal radiation damage. The structure sets a standard for room-temperature refinement of macromolecular targets and provides accurate data for modeling protein–solvent interactions.

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL. Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydro­phobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.