Method specific

Fit of model and data (X-ray and cryo-EM specific)

This section, primarily for X-ray and cryo-EM, details how well the atomic model fits the experimental electron density map. For X-ray, you’ll find details on RSRZ outliers, indicating residues with poor fit to density. For cryo-EM, it will include Q-score summaries, showing how well atoms are resolved and fit within the EM map.

NMR specific

Chemical shifts validation

This section is unique to NMR reports. It provides details on Assignment Completeness (how many chemical shifts have been assigned) and lists Statistically Unusual Chemical Shifts, which can point to interesting structural features or potential errors in assignment.

Ensemble composition and analysis

This section provides details about the NMR ensemble, including the RMSD to mean structure/ensemble, which indicates the precision and conformational variability of the determined structure.

NMR restraints analysis

This crucial section for NMR structures details the experimental restraints. You’ll find:

• Conformationally restricting restraints. A summary of the types and numbers of distance and dihedral angle restraints used. It often includes the number of restraints per residue.
• Residual restraint violations. Tables and graphs summarising the number and magnitude of distance and dihedral angle violations across the ensemble of models. Pay close attention to consistently violated restraints (those violated in more than one model) and large violations, as these indicate inconsistencies with the experimental data.
• Distance/Dihedral-angle violation analysis. Remember that NMR structures are often represented by an ensemble of multiple models. Each of these models should ideally satisfy the experimental data. The report will tell you how many models in the ensemble violate a particular restraint. If a restraint is violated in all or a high percentage of the models within the ensemble, that’s a red flag. This could suggest a fundamental problem with the model in that region or a potential misinterpretation of the experimental data.

The number of restraint violations listed in a PDB entry can differ from what was obtained during structure calculation. This is because all violations are independently recalculated by the PDB during the deposition process, which may use different software or thresholds.

The results are reported and binned into small, medium, and large violation categories based on the magnitude of the violation values. In each bin, the average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble. The maximum value of the violation in each bin is also reported.

You’ll find tables summarising “Consistently violated” restraints in the “Summary of distance violations” and “Summary of dihedral-angle violations”.

The report also lists the “Most violated distance restraints” and “Most violated dihedral angle restraints”. If a critical region of the protein has many highly violated restraints, it indicates that the model is not well-supported by the experimental data in that area. This is particularly useful if this falls in the region that you are interested in.