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Validation slider

On the main entry page for each PDB ID, you will find a graphical “Validation” summary, often presented as a slider. This visual summary quickly shows you how the structure’s key global metrics (e.g. R-free, clashscore and outlier percentages) compare to those of other structures in the PDB.

The black square reports on how the given entry ranks relative to all structures in the PDB. The white or open slider reports on the comparison with structures derived using the same technique (X-ray structures are compared with other X-ray structures solved at a similar resolution, while NMR and EM structures are ranked relative to other NMR and EM structures in the PDB, respectively).

In general, you would want all sliders to lie far to the right in the blue areas, indicating “Better” quality (especially for recently determined structures, and particularly the resolution-specific sliders).

While the slider provides a useful snapshot and comparison, it does not provide the detailed information needed for a thorough assessment.

PDB ID: 2xhh. This validation slider represents an excellent example of a high-quality X-ray crystal structure. All metrics (R-free, Clashscore, Ramachandran outliers, Sidechain outliers, and RSRZ outliers) show their markers positioned far into the blue “Better” region. Both the black (comparison to all X-ray structures) and white (comparison to X-ray structures of similar resolution) indicators are well to the right, signifying that this structure performs exceptionally well across all key validation criteria relative to other entries in the PDB.

PDB ID: 3lnn. This validation slider demonstrates an example of a low-quality X-ray crystal structure with significant validation issues. The R-free value is notably high (0.337), and the Clashscore is very high at 49. Crucially, the Ramachandran outliers are at 10.3% and Sidechain outliers at 17.7%. All markers are shifted considerably into the red “Worse” region, indicating that this structure performs poorly across nearly all metrics when compared to other X-ray structures, even those of similar resolution. This structure should be interpreted with caution and subjected to thorough re-evaluation before being used for any scientific conclusions.