Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.

ABSTRACT

A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Šfor trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Šfor subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Šfor lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Šand thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Šresolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Šresolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.