Identifying dynamic, partially occupied residues using anomalous scattering

Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1084-1095. doi: 10.1107/S2059798319014475. Epub 2019 Nov 19.


Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.

Keywords: anomalous scattering; chaperones; crystallography; partially occupied residues; protein dynamics; protein folding.

MeSH terms

  • Carrier Proteins / chemistry*
  • Crystallization / methods*
  • Crystallography, X-Ray / methods*
  • Escherichia coli Proteins / chemistry*
  • Kinetics
  • Models, Molecular
  • Molecular Chaperones / chemistry*
  • Periplasmic Proteins / chemistry*
  • Protein Conformation


  • Carrier Proteins
  • E colicin-binding immunity protein Im7, E coli
  • Escherichia coli Proteins
  • Molecular Chaperones
  • Periplasmic Proteins
  • Spy protein, E coli