Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

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...

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: 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: 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...

Molecular Models

Molecular Models

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.

You might also read

Related Articles

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

Sort by

Same author

Irradiation does not impact the immunogenicity of food flours used for oral immunotherapy.

The journal of allergy and clinical immunology. Global·2026

Same author

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

PLoS computational biology·2026

Same author

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].

Living journal of computational molecular science·2026

Same author

New targets and procedures for validating the valence geometry of nucleic acid structures.

Nucleic acids research·2026

Same author

Structures of human protein tyrosine phosphatase variants reveal targetable allosteric sites.

The Journal of biological chemistry·2025

Same author

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures: near-predictive, pseudostructure and barbed wire.

Acta crystallographica. Section D, Structural biology·2025

Same journal

Structural insights into the synthesis of FMN in prokaryotic organisms.

Acta crystallographica. Section D, Biological crystallography·2015

Same journal

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Acta crystallographica. Section D, Biological crystallography·2015

Same journal

Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals.

Acta crystallographica. Section D, Biological crystallography·2015

Same journal

The first crystal structure of the peptidase domain of the U32 peptidase family.

Acta crystallographica. Section D, Biological crystallography·2015

Same journal

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Acta crystallographica. Section D, Biological crystallography·2015

Same journal

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.

Acta crystallographica. Section D, Biological crystallography·2015

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 17, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

MolProbity: all-atom structure validation for macromolecular crystallography.

Vincent B Chen¹, W Bryan Arendall, Jeffrey J Headd

¹Department of Biochemistry, Duke University, Durham, NC 27710, USA.

Acta Crystallographica. Section D, Biological Crystallography

|January 9, 2010

Summary

This summary is machine-generated.

MolProbity is a web service for validating protein and nucleic acid structures, identifying and correcting errors. Recent enhancements improve its accuracy and impact on the global structural database.

More Related Videos

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

Related Experiment Videos

Last Updated: Jun 17, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

Area of Science:

Structural Biology
Biochemistry
Computational Biology

Background:

X-ray crystallography advances enable easier structure determination, but local errors persist even in high-resolution models.
These errors, including Ramachandran outliers and incorrect sugar puckers, can impact biological interpretations.
Reliable methods are crucial for crystallographers and end-users to diagnose and correct these structural inaccuracies.

Purpose of the Study:

To review the capabilities of MolProbity, a structure-validation web service.
To report on recent enhancements and usage of MolProbity.
To present evidence of MolProbity's positive impact on the global structural database.

Main Methods:

MolProbity utilizes optimized hydrogen placement and all-atom contact analysis.
It incorporates updated covalent-geometry and torsion-angle criteria for comprehensive evaluation.
Diagnostics are presented graphically to aid manual model rebuilding.

Main Results:

MolProbity provides broad-spectrum evaluation of model quality at global and local levels.
Some local corrections can be automated within the MolProbity service.
Recent improvements demonstrate a beneficial effect on the global structural database.

Conclusions:

MolProbity is an essential tool for diagnosing and correcting errors in protein and nucleic acid structures.
Its continuous development and enhancements contribute to improved structural data quality.
The service plays a vital role in ensuring the reliability of biologically important molecular data.