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X-ray Crystallography

X-ray Crystallography

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...

Crystallographic Point Groups

Crystallographic Point Groups

Crystallographic point groups represent the various symmetry operations that can occur within crystals. They are unique in that at least one point will always remain unchanged during these actions. For instance, consider the triclinic system. This system, devoid of any axis or plane of symmetry, aligns with the C1 and Ci point groups.where Cᵢ is characterized solely by a center of inversion.Contrastingly, the monoclinic system introduces an element of symmetry. This system with one plane and...

Determination of Crystal Structures

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...

Imperfections in Crystal Structure: Point, Line and Plane Defects

Imperfections in Crystal Structure: Point, Line and Plane Defects

A perfect crystal, in theory, has a uniform structure with the same unit cell and lattice points throughout. However, any deviation from this periodic arrangement is known as an imperfection or defect. These defects can be categorized into three types: point, line, and plane defects.Point defects occur when there is a deviation from the ideal due to missing atoms, displaced atoms, or additional atoms. These imperfections might occur due to imperfect packing during crystallization or because of...

Imperfections in Crystal Structure: Stoichiometric Point Defects

Imperfections in Crystal Structure: Stoichiometric Point Defects

Schottky defects arise when some lattice points in a crystal, such as those in NaCl, remain unoccupied, creating lattice vacancies without disturbing the overall electrical neutrality of the crystal. This defect is common in ionic crystals where the positive and negative ions are similar in size, as seen in sodium chloride and cesium chloride. The presence of Schottky defects enables the crystal to conduct electricity to a small extent through an ionic mechanism. Electric fields cause nearby...

Imperfections in Crystal Structure: Non-Stoichiometric Defects

Imperfections in Crystal Structure: Non-Stoichiometric Defects

Non-stoichiometric defects refer to a type of defect in the crystal structure of a compound where the ratio of its constituent elements deviates from the ideal stoichiometric ratio. There are two main types of non-stoichiometric defects: metal excess defects and metal deficiency defects.Metal excess defects occur when there is a slight surplus of metal ions than what is required by the stoichiometric ratio of the compound. For example, heating a sodium chloride crystal in sodium vapor results...

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Related Experiment Video

Updated: Jun 9, 2026

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Published on: March 13, 2021

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.

Lucrezia Catapano¹, Fei Long², Keitaro Yamashita²

¹Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom.

Acta Crystallographica. Section D, Structural Biology

|November 3, 2023

Summary

Neutron crystallography can now visualize most hydrogen atoms in macromolecules using enhanced REFMAC5 software. This method improves structural accuracy, especially for protonation states, overcoming limitations of X-ray crystallography.

Keywords:

CCP4 H atoms REFMAC5 crystallographic refinement neutron macromolecular crystallography

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Last Updated: Jun 9, 2026

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Optimization of Crystal Growth for Neutron Macromolecular Crystallography

Published on: March 13, 2021

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

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

Published on: December 1, 2020

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Hydrogen atoms are crucial for macromolecular functions like enzyme catalysis and protein interactions.
X-ray crystallography struggles to visualize most hydrogen atoms, limiting understanding of protonation states.
Neutron diffraction, particularly with deuterium, effectively visualizes hydrogen atoms at common resolutions.

Purpose of the Study:

To extend the REFMAC5 program for refining macromolecular models using neutron crystallographic data.
To incorporate accurate stereochemical restraints for hydrogen atoms into the CCP4 Monomer Library.
To introduce and test a new feature for refining the protium/deuterium fraction in neutron diffraction analysis.

Main Methods:

Extension of REFMAC5 algorithms to process neutron crystallographic data.
Inclusion of stereochemical restraints for hydrogen atoms within the CCP4 Monomer Library.
Development of a protium/deuterium fraction refinement parameter for neutron scattering.
Testing the enhanced REFMAC5 on existing PDB entries and a novel structure (FutA) using neutron data alone or with X-ray restraints.

Main Results:

The re-refinement of structures using the enhanced REFMAC5 yielded R-factor values comparable to or better than original depositions.
The newly incorporated stereochemical restraints and protium/deuterium fraction refinement improved model accuracy.
Using external reference structure restraints proved beneficial, particularly for medium-to-low resolution structures.

Conclusions:

The extended REFMAC5 program effectively refines macromolecular models from neutron crystallographic data.
This advancement facilitates more accurate determination of hydrogen atom positions and protonation states.
Neutron crystallography, supported by enhanced computational tools like REFMAC5, is a powerful method for detailed structural analysis.