Dear All, > RMSD of ensemble of NMR structures can be interpreted as the > uncertainty of coordinates. Core residues of NMR structures have > smaller RMSDs in a similar way that core residues of crystal > structures have relatively smaller B-factors compared to surface > residues. The problem with the ensemble RMSD in NMR is that it depends on the refinement protocol. It is very important that the ensemble is refined to the highest possible RMSD while still fitting the experimental data (typically the distance restrants from NOEs and torsion angle restraints from J-couplings). Unfortunately, people are still looking at the RMSD as a measure of model quality. That is similar to looking only at the X-ray resolution to assess the quality of a structure model.
> Both x-ray and NMR approaches can reveal "atomic resolution > structures" but precision and quality of structures should be varying > depending on individual examples. That is why one should use validation scores based on a set of measurements not used in the refinement like R-free (X-ray) or residual dipolar couplings (NMR). But even then one should always look at the structure model in the context of the experimental data. High resolution/low R-free X-ray structure models can still have serious problems. There are loads of examples in the EDS (especially around ligands). Cheers, Robbie Joosten Centre for Molecular and Biomolecular Informatics
