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Related Concept Videos

Determination of Crystal Structures01:29

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...
X-ray Crystallography02:18

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...
Imperfections in Crystal Structure: Point, Line and Plane Defects01:25

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...
Crystallographic Point Groups01:29

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...
Imperfections in Crystal Structure: Stoichiometric Point Defects01:26

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 Defects01:29

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: May 20, 2026

Microcrystallography of Protein Crystals and In Cellulo Diffraction
09:35

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space

Thomas C Terwilliger1, Randy J Read, Paul D Adams

  • 1Bioscience Division and Los Alamos Institutes, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

Acta Crystallographica. Section D, Biological Crystallography
|July 4, 2012
PubMed
Summary

This study introduces a density-guided method to rebuild protein models after molecular replacement. It refines models even when initial templates significantly differ from the target structure.

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

Published on: December 1, 2020

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Last Updated: May 20, 2026

Microcrystallography of Protein Crystals and In Cellulo Diffraction
09:35

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

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

Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Biology

Background:

  • Molecular replacement (MR) is crucial for determining protein structures.
  • Model rebuilding challenges arise when MR search models have high root-mean-square deviation (r.m.s.d.) from the target structure.
  • Existing methods struggle with significant template-target structural differences.

Purpose of the Study:

  • To develop an automated approach for model rebuilding after molecular replacement.
  • To improve the accuracy of protein structure determination when initial models are dissimilar to the target.
  • To extend the applicability of automated model building and refinement.

Main Methods:

  • A density-guided procedure for template deformation was introduced.
  • Residue coordinate shifts were calculated by optimizing local model density against electron-density maps.
  • The process involved iterative cycles of local deformation, refinement, and map recalculation.

Main Results:

  • The method successfully deformed placed templates to better match electron-density maps.
  • Local template deformation improved model-map correlation.
  • The procedure enabled automated model building and refinement for search models with >2 Å r.m.s.d.

Conclusions:

  • This density-guided deformation approach enhances automated model rebuilding in crystallography.
  • It significantly extends the utility of molecular replacement for challenging structures.
  • The method facilitates the determination of protein structures from dissimilar search models.