Deviations from standard atomic volumes as a quality measure for protein crystal structures

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Protein crystal structure quality assessment is crucial for reliable biological insights.
• Traditional methods may not capture subtle model inaccuracies.
• Atomic and residue volumes offer a potentially sensitive, independent validation metric.

Purpose of the Study:

• To develop and validate a new method for assessing protein crystal structure quality using atomic and residue volumes.
• To establish volume Z-scores and Z-score root mean square deviation (Z-score rms) as indicators of structural accuracy.
• To correlate volume-based metrics with established quality indicators like resolution and R-factor.

Main Methods:

• Computation of standard atomic and residue volumes using the Voronoi procedure in 64 protein crystal structures.
• Calculation of volume Z-scores to quantify deviations of individual atomic volumes.
• Determination of Z-score rms for global structure quality assessment and outlier identification.

Main Results:

• Z-score rms correlates inversely with crystallographic resolution and R-factor, indicating better quality with improved parameters.
• Volume-based outlier detection successfully identified structures with unusual stereochemistry.
• Individual atomic Z-scores > 3 pinpointed problematic regions, correlating with B-factors and PROCHECK-identified stereochemical issues.

Conclusions:

• Atomic and residue volumes provide an independent and sensitive measure for protein structure validation.
• The PROVE program, implementing these volume-based procedures, offers a valuable tool for structure quality control.
• This method enhances the reliability of structural models derived from X-ray crystallography.