The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure

The size of the protein database (PDB) makes it now feasible to arrive at statistical conclusions regarding structural effects of crystal packing. These effects are relevant for setting upper practical limits of accuracy on protein modeling. Proteins whose crystals have more than one molecule in the asymmetric unit or whose structures were determined at least twice by X-ray crystallography were paired and their differences analyzed. We demonstrate a clear influence of crystal environment on protein structure, including backbone conformations, hinge-like motions and side-chain conformations. The positions of surface water molecules tend to be variable in different crystal environments while those of ligands are not. Structures determined by independent groups vary more than structures determined by the same authors. The use of different refinement methods is a major source for this effect. Our pair-wise analysis derives a practical limit to the accuracy of protein modeling. For different crystal forms, the limit of accuracy (Cα, root-mean-square deviation (RMSD)) is ∼0.8 Å for the entire protein, which includes ∼0.3 Å due to crystal packing. For organized secondary elements, the upper limit of Cα RMSD is 0.5–0.6 Å while for loops or protein surface it reaches 1.0 Å. Twenty percent of exposed side- chains exhibit different χ1+2 conformations with approximately half of the effect also resulting from crystal packing. A web based tool for analysis and graphic presentation of surface areas of crystal contacts is available ().