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Microcrystallography of Protein Crystals and In Cellulo Diffraction
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Percentile-based spread: a more accurate way to compare crystallographic models
1University of Maryland, Baltimore, USA. epozhars@rx.umaryland.edu
Acta Crystallographica. Section D, Biological Crystallography
|September 9, 2010
Summary
The percentile-based spread (p.b.s.) offers a more robust method for comparing biomacromolecular crystal structures than traditional root-mean-square distance. This new measure better represents average atomic variations, even with outliers present.
Area of Science:
- Structural biology
- Biophysics
- Crystallography
Background:
- Biomacromolecular crystal structure comparison traditionally uses root-mean-square distance (RMSD).
- RMSD is sensitive to outliers, disproportionately affecting the comparison.
- A need exists for a more robust measure of structural variation.
Purpose of the Study:
- To introduce and validate the percentile-based spread (p.b.s.) as an alternative to RMSD.
- To demonstrate p.b.s.'s effectiveness in representing average atomic position variations.
- To evaluate p.b.s. in diverse crystallographic contexts.
Main Methods:
- Development of the percentile-based spread (p.b.s.) metric.
- Application of p.b.s. to compare biomacromolecular crystal structures.
- Analysis of p.b.s. performance with simulated and real crystallographic data.
Main Results:
- The percentile-based spread (p.b.s.) provides a more adequate representation of average atomic position variation.
- p.b.s. is less sensitive to outliers compared to traditional RMSD.
- p.b.s. is applicable to isomorphous structures, conformational changes, and model ensembles.
Conclusions:
- The percentile-based spread (p.b.s.) is a superior metric for comparing biomacromolecular crystal structures.
- p.b.s. offers enhanced accuracy and robustness, particularly in the presence of data variations.
- This method improves the analysis of structural dynamics and ensemble data in crystallography.
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