Hands-on: Interpreting the PDB validation slider

In the previous sections, we’ve explored the various metrics used to assess the quality of macromolecular structures, such as R-free, Clashscore, and Ramachandran outliers. The wwPDB provides a powerful visual tool, the Validation Slider, which condenses these complex metrics into an easily digestible graphical summary. This slider allows for a quick assessment of a structure’s global quality by comparing it against a vast dataset of all deposited structures and, more specifically, against structures determined by the same experimental method and at similar resolutions.

A “good” structure will typically show its metrics in the blue “Better” region, indicating favourable stereochemistry and agreement with experimental data. Conversely, metrics in the red “Worse” region signal potential issues that warrant closer examination.

This hands-on activity will guide you through the process of locating and interpreting the PDB Validation Slider for a specific entry, allowing you to practice assessing global quality metrics in a practical setting.

Instructions

1. Go to the PDBe website (https://www.ebi.ac.uk/pdbe/) and search for entry 3AM7.
2. Locate the “Validation” summary (slider graphic) on the main entry page. If you are visiting the new entry pages, go to the “Model quality” tab to see the slider.
3. Identify the “R-free” value and its percentile rank (black square and open slider). Is it in the “Better” (blue) or “Worse” (red) region compared to all X-ray structures and X-ray structures of similar resolution? 
4. Repeat this for the “Clashscore” and “Ramachandran outliers” metrics. 

Based on these three metrics, would you consider this structure to have generally good, average, or poor global quality?