Related Experiment Video
Updated: Feb 2, 2026

Crystallization of Proteins on Chip by Microdialysis for In Situ X-ray Diffraction Studies
Published on: April 11, 2021
Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment
Ivan G Shabalin1,2, Przemyslaw J Porebski1,2, Wladek Minor1,2
1Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.
Abstract:
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
More Related Videos
07:55An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering
Published on: July 6, 2019
08:44Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
Published on: August 22, 2017
Related Concept Videos
X-ray Diffraction of Biological Samples
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are scattered by the electron clouds around the sample atoms. The X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...
X-ray Crystallography
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
Data Collection by Experiments
An example of the experimental method is a public...
Interference and Diffraction
Model Approaches for Pharmacokinetic Data: Physiological Models
Model Approaches for Pharmacokinetic Data: Compartment Models
Two primary types of compartment models are recognized: mammillary and catenary. The more...