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View Crystal Structure Quality in 3D

09/20

A new Mol* 3D option displays PDB structures determined with X-ray crystallography using a coloring scheme similar to what is used to show Computed Structure Models confidence levels. This feature is available for most crystal structures in the PDB with structure factors.

<I>Mol* view of PDB structure <a href="https://www.rcsb.org/3d-view/1DTJ">1dtj</a>. To select this coloring scheme, select the “Experimental Support Confidence” option under Quality Assessment.</I>Mol* view of PDB structure 1dtj. To select this coloring scheme, select the “Experimental Support Confidence” option under Quality Assessment.

This display option was developed using individual-residue Real Space Correlation Coefficient (RSCC) values that indicate how well the atomic coordinates for an individual residue are supported by X-ray crystallographic experimental data. Individual RSCC values vary with both residue chemical structure and structure resolution. Therefore, the RSCC values for each type of amino acid in PDB X-ray structures at different resolutions were ranked from lowest to highest, indicating worse to better experimental data support for residue atomic coordinates.

Amino acid residues in any PDB structure are colored by their RSCC value ordinal ranking as follows:

  • Blue (25-100%): very well resolved residues, very high confidence
  • Cyan (5-25%): well resolved residues, high confidence
  • Yellow (1-5%): outlier residues, low confidence
  • Orange (<1%): extreme outlier residues, very low confidence

With the RSCC-based confidence score and color scheme, RSCC outliers are readily apparent in ribbon representation 3D graphical displays, in a color scheme consistent with the pLDDT (predicted lDDT-Cα)-based confidence coloring scheme used for Computed Structure Models.

For a description of how the quality measures were developed, see

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level, Structure (2022) doi: 10.1016/j.str.2022.08.004

This study also demonstrates that while RSCC values in a crystal structure are correlated with pLDDT scores in the corresponding AlphaFold2 model, crystal structures in the PDB are generally more reliable than AlphaFold2 models.

Mol* also supports a coloring scheme based on wwPDB Validation Reports that indicates the number of geometry related problems for a specific residue (e.g., geometry outliers, and clashes).

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