Related Experiment Video
Updated: Jul 16, 2025
09:35
Microcrystallography of Protein Crystals and In Cellulo Diffraction
Published on: July 21, 2017
9.1K
MatchMaps: Non-isomorphous difference maps for X-ray crystallography.
Dennis E Brookner1, Doeke R Hekstra1,2
1Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA.
Biorxiv : the Preprint Server for Biology
|September 21, 2023
Summary
This study introduces MatchMaps, a Python package for calculating observed difference electron density maps. MatchMaps enhances sensitivity to macromolecular conformational changes, even in challenging crystal conditions.
Area of Science:
- Structural biology
- Biophysics
- Computational biology
Background:
- Macromolecular conformational changes are vital for biological functions.
- Crystallography is a powerful tool for mapping these structural changes.
- Isomorphous difference maps are sensitive but susceptible to crystal imperfections.
Approach:
- Developed a generalized procedure for calculating observed difference maps.
- Implemented this procedure in an open-source Python package, MatchMaps.
- MatchMaps integrates with PHENIX and CCP4 software environments.
Key Points:
- MatchMaps retains high sensitivity to conformational changes without requiring refinement of the perturbed state.
- The package effectively "rescues" difference maps from poorly-isomorphous crystals.
- It corrects artifacts in standard isomorphous difference maps and detects subtle structural variations.
Conclusions:
- MatchMaps offers a robust method for analyzing structural differences in crystallography.
- This tool improves the detection of conformational dynamics across various experimental setups.
- It extends difference map analysis to intra- and inter-crystal form comparisons.
Related Concept Videos
02:18X-ray Crystallography
24.0K
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed 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...
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...
24.0K
01:10X-ray Diffraction of Biological Samples
3.8K
X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
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...
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...
3.8K
02:52Stereoisomerism
12.0K
Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric isomers, in which the same atoms are connected through the same types of bonds but with differences in their orientation in space. Coordination complexes with two different ligands in the cis and trans positions from a ligand of interest form isomers. For example, the octahedral [Co(NH3)4Cl2]+ ion has two isomers (Figure 1) In the cis...
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric isomers, in which the same atoms are connected through the same types of bonds but with differences in their orientation in space. Coordination complexes with two different ligands in the cis and trans positions from a ligand of interest form isomers. For example, the octahedral [Co(NH3)4Cl2]+ ion has two isomers (Figure 1) In the cis...
12.0K