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Related Concept Videos

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...
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...
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...
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...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

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 crystal...

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Updated: May 19, 2026

Microcrystallography of Protein Crystals and In Cellulo Diffraction
09:35

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

CheShift-2 resolves a local inconsistency between two X-ray crystal structures.

Jorge A Vila1, Shih-Che Sue, James S Fraser

  • 1Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Journal of Biomolecular NMR
|September 5, 2012
PubMed
Summary
This summary is machine-generated.

The CheShift-2 web server accurately validated protein structures using chemical shifts, resolving inconsistencies between X-ray crystallography models of NFκB and IκBα. This tool aids in refining protein structure determination.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Chemical shifts offer valuable insights into protein structure in solution.
  • The CheShift-2 web server was developed for structure interrogation using a quantum mechanics database of (13)C(α) chemical shifts.

Purpose of the Study:

  • To apply the CheShift-2 server to resolve a local structural inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) of the NFκB-IκBα complex.
  • To validate the CheShift-2 server's performance using available NMR resonance assignments.

Main Methods:

  • Utilized the CheShift-2 web server for structure interrogation based on (13)C(α) chemical shifts.
  • Applied NMR resonance assignments for independent validation.
  • Performed recalculation of local structure based on X-ray structure factors.

Main Results:

  • CheShift-2 analysis confirmed that chemical shifts for the Gly270-Pro281 sequence in IκBα were consistent with the 1IKN structure, not 1NFI.
  • NMR data and structural recalculations supported 1IKN for backbone structure but indicated the 1NFI rotamer for Trp258 was plausible.
  • A hydrogen bond between Trp258 and Gln278 was identified, consistent with the 1NFI structure.

Conclusions:

  • The CheShift-2 server effectively validates protein structures when backbone chemical shifts are available.
  • The server performs well even when local plasticity makes X-ray structural data ambiguous.
  • This study highlights the utility of CheShift-2 in reconciling structural data from different experimental methods.