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Updated: Feb 11, 2026

Crystallizing Membrane Proteins for Structure Determination using Lipidic Mesophases
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RABDAM: quantifying specific radiation damage in individual protein crystal structures.

Kathryn L Shelley1, Thomas P E Dixon1, Jonathan C Brooks-Bartlett1

  • 1Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

Journal of Applied Crystallography
|April 17, 2018
PubMed
Summary

Radiation damage impacts protein crystallography (PX) structure accuracy. A new program, RABDAM, quantifies site-specific radiation damage using the B_Damage metric, aiding in assessing and improving PDB structure quality.

Keywords:
BDamagePDBProtein Data BankRABDAMatomic B factorsatomic displacement parameterscomputer programsprotein crystallographyradiation damage

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Area of Science:

  • Structural Biology
  • Biophysics
  • Crystallography

Background:

  • Radiation damage is a significant challenge in protein crystallography (PX), limiting accurate structure determination.
  • High-flux synchrotron X-ray sources can induce substantial radiation damage, even with cryo-cooling.
  • Identifying site-specific structural changes caused by radiation damage has been historically difficult.

Purpose of the Study:

  • To present RABDAM, a novel program for calculating the B_Damage metric.
  • To enable quantitative assessment of site-specific radiation damage in protein structures.
  • To improve the quality of structures in the Protein Data Bank (PDB).

Main Methods:

  • Development of the B_Damage metric, which compares atomic B-factors in similar local environments.
  • Implementation of the RABDAM program to calculate B_Damage for all atoms in PDB or mmCIF files.
  • Utilizing RABDAM to provide outputs for assessing radiation damage extent.

Main Results:

  • RABDAM successfully calculates the B_Damage metric for protein structures.
  • The program provides quantitative data to identify potential sites of radiation damage.
  • Outputs from RABDAM facilitate the assessment of radiation damage in PX structures.

Conclusions:

  • RABDAM is a valuable free and open-source tool for assessing radiation damage in protein crystallography.
  • The software aids in evaluating and enhancing the quality of existing and new PDB structures.
  • Quantitative B_Damage analysis can help mitigate limitations imposed by radiation damage.