Putting it all together

When you’re focusing on a specific region of a structure, use the global metrics to get an initial sense of the overall quality, and then combine visual inspection in a molecular viewer with the detailed information in the Validation Report to answer these crucial local questions:

• In x-ray crystallography structures, does the experimental density clearly support the model in this region (backbone, side chains, ligand)? Look for the 2mFo-DFc density tracing the model and check difference maps (mFo-DFc) for unexplained positive (green) or negative (red) density.
• Are there stereochemical outliers (Ramachandran, sidechain, bond/angle) in this region? If so, is there strong experimental evidence (clear density) to support the unusual geometry, or does it seem like a modelling error?
• Are there significant clashes in or near this region? If so, do they correlate with poor density fit or other issues?
• If there’s a ligand, does it fit the density well for all atoms (visually, and based on RSCC and RSR values)? Is its stereochemistry plausible? Are there signs of partial occupancy or multiple conformations?
• Is this region modelled despite weak or missing experimental density? If so, be aware of the lower confidence in its accuracy.
• For NMR structures, check for restraint violations in this region. Restraint violations occur when the calculated atomic distances or angles in the model do not satisfy the experimental constraints derived from NMR data (e.g., NOE distance restraints or dihedral angle restraints). These violations indicate that the model is inconsistent with the experimental data and suggest potential inaccuracies in the local structure. Additionally, examine the ensemble to see how well-defined a local region is; a tightly clustered ensemble in a specific area suggests higher confidence in that region’s conformation.

By systematically applying these visual and metric-based checks to your region of interest, you can make an informed judgment about the local reliability of the structural model for your specific research application.