The PDZ2 Domain of Syntenin at Ultra-high Resolution: Bridging the Gap Between Macromolecular and Small Molecule Crystallography

Abstract

The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 Å resolution. The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and R free of 8.7%, making it the most precise crystallographic model of a protein molecule to date. The model reveals discrete disorder in several places in the molecule, and significant plasticity of the peptide bond, with some ω angles deviating by nearly 20° from planarity. Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C–H⋯O type are clearly visible between the β-strands. The study sets a new standard for high-resolution protein crystallography.