The war of tools: how can NMR spectroscopists detect errors in their structures?
Edoardo Saccenti and Antonio Rosato
Journal of Biomolecular NMR; 2008; 40(4) pp 251 - 261
Abstract:
Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 Å, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. ϕ–ψ distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.