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Updated: Jun 25, 2026
07:19
Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
Published on: November 5, 2018
Scotty: lattice coincidences in the Protein Data Bank
Airlie J McCoy1, Lawrence C Andrews2, Herbert J Bernstein3
1Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom.
Acta Crystallographica. Section D, Structural Biology
|June 24, 2026
Summary
Lattice analysis of protein data reveals common crystal packing and highlights inconsistencies in biological assembly annotations. This study offers insights into macromolecular self-association and protein crystal structures.
Area of Science:
- Structural Biology
- Biophysics
- Crystallography
Background:
- Crystallographic data in the Protein Data Bank (PDB) is crucial for understanding molecular structures.
- Analysis of crystal packing (lattice coincidences) can reveal relationships between different entries.
Purpose of the Study:
- To perform a PDB-wide analysis of lattice coincidences using the Scotty application.
- To investigate the implications of lattice clustering for understanding protein structures and biological assemblies.
Main Methods:
- Utilized the Scotty application within the Phasertng codebase for PDB-wide lattice coincidence analysis.
- Defined lattice coincidence broadly to identify distinct lattice clusters.
- Combined lattice clustering with sequence identity and oligomeric annotations.
Main Results:
- Approximately half of all PDB entries fall into distinct lattice clusters.
- Over a thousand lattice clusters contain entries from different space groups, indicating pseudo-symmetric variations.
- Lattice-level space-group frequencies provide more accurate priors for novel crystal forms than entry-based counts.
- Identified inconsistencies in biological assembly assignments for structures with near-identical lattices.
- Discovered various protein systems forming paracrystalline arrays, including storage, sequestration, toxin, and membrane-associated proteins.
Conclusions:
- Lattice-level analysis offers a valuable perspective on macromolecular self-association.
- The findings suggest opportunities for improving structural annotations in the PDB.
- Highlights an understudied area of structural biology concerning in cellulo paracrystalline arrays.
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