Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?

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Abstract
We have compared structures of 78 proteins determined by both NMR and X‐ray methods. It is shown that X‐ray and NMR structures of the same protein have more differences than various X‐ray structures obtained for the protein, and even more than various NMR structures of the protein. X‐ray and NMR structures of 18 of these 78 proteins have obvious large‐scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small‐scale differences comparable with differences between various X‐ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X‐ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X‐ray structures at distances below 3.0 Å and 4.5–6.5 Å, and fewer contacts at distances of 3.0–4.5 Å and 6.5–8.0 Å; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for β‐containing proteins than for all‐α proteins. Another significant difference is that the main‐chain hydrogen bonds identified in X‐ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X‐ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results. Proteins 2005.