On interpretation of protein X-ray structures: Planarity of the peptide unit

Pauling's mastery of peptide stereochemistry-based on small molecule crystal structures and the theory of chemical bonding-led to his realization that the peptide unit is planar and then to the Pauling-Corey-Branson model of the α-helix. Similarly, contemporary protein structure refinement is based on experimentally determined diffraction data together with stereochemical restraints. However, even an X-ray structure at ultra-high resolution is still an under-determined model in which the linkage among refinement parameters is complex. Consequently, restrictions imposed on any given parameter can affect the entire structure. Here, we examine recent studies of high resolution protein X-ray structures, where substantial distortions of the peptide plane are found to be commonplace. Planarity is assessed by the ω-angle, a dihedral angle determined by the peptide bond (C-N) and its flanking covalent neighbors; for an ideally planar trans peptide, ω = 180°. By using a freely available refinement package, Phenix [Afonine et al. (2012) Acta Cryst. D, 68:352-367], we demonstrate that tightening default restrictions on the ω-angle can significantly reduce apparent deviations from peptide unit planarity without consequent reduction in reported evaluation metrics (e.g., R-factors). To be clear, our result does not show that substantial non-planarity is absent, only that an equivalent alternative model is possible. Resolving this disparity will ultimately require improved understanding of the deformation energy. Meanwhile, we urge inclusion of ω-angle statistics in new structure reports in order to focus critical attention on the usual practice of assigning default values to ω-angle constraints during structure refinement.