Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

25.6K
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...
25.6K
Molecular Models02:00

Molecular Models

43.2K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

NrdR-a unique nucleotide-sensing regulator of prokaryotic ribonucleotide reductases.

Microbiology and molecular biology reviews : MMBR·2026
Same author

A truncated CDC14A retains catalytic structure and phosphatase activity preserving male fertility but causes nonsyndromic deafness.

The Journal of biological chemistry·2025
Same author

Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15.

Nature communications·2025
Same author

A single residue affects the dynamics and shape of a tetrameric GH43 β-1,4-d-xylosidase from Levilactobacillus brevis DSM1269.

Protein science : a publication of the Protein Society·2025
Same author

Identification of chemical scaffolds for targeting ubiquitin-specific protease 11 (USP11) through high-throughput virtual screening.

Journal of enzyme inhibition and medicinal chemistry·2025
Same author

Author Correction: Nanomolar inhibitor of the galectin-8 N-terminal domain binds via a non-canonical cation-π interaction.

Communications chemistry·2025

Related Experiment Video

Updated: Dec 27, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.5K

Interactive model building in neutron macromolecular crystallography.

Derek T Logan1

  • 1Section for Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden.

Methods in Enzymology
|February 26, 2020
PubMed
Summary

This guide introduces interactive model building in macromolecular neutron crystallography for X-ray crystallographers. It covers software, nuclear density maps, and data deposition for joint neutron/X-ray structures.

Keywords:
Model buildingModel refinementNeutron macromolecular crystallographyNuclear density mapsPerdeuterated proteinsProtein Data Bank

More Related Videos

Optimization of Crystal Growth for Neutron Macromolecular Crystallography
12:29

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Published on: March 13, 2021

5.8K
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.2K

Related Experiment Videos

Last Updated: Dec 27, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.5K
Optimization of Crystal Growth for Neutron Macromolecular Crystallography
12:29

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Published on: March 13, 2021

5.8K
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

10.2K

Area of Science:

  • Structural Biology
  • Biophysics
  • Crystallography

Background:

  • Macromolecular crystallography traditionally relies on X-ray diffraction.
  • Neutron crystallography offers complementary information, particularly for hydrogen atoms.
  • Integrating neutron data with X-ray data presents unique challenges in model building.

Purpose of the Study:

  • To provide an overview of interactive model building in macromolecular neutron crystallography.
  • To guide researchers transitioning from X-ray crystallography to neutron crystallography.
  • To address practical aspects of using common software and data deposition.

Main Methods:

  • Utilizing phenix.refine for refinement and Coot for model building as examples.
  • Describing work-arounds for program communication.
  • Explaining the interpretation of nuclear density maps versus electron density maps.

Main Results:

  • Demonstrated practical steps for interactive model building using specific software.
  • Highlighted differences between nuclear and electron density maps.
  • Provided guidance for depositing combined neutron/X-ray structural data.

Conclusions:

  • Interactive model building in neutron crystallography is achievable for X-ray crystallographers.
  • Understanding density map differences and software interactions is key.
  • Facilitating data deposition aids the integration of neutron and X-ray structural data.