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Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

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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...
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Determination of Crystal Structures01:29

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

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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...
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VSEPR Theory for Determination of Electron Pair Geometries
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Transformation of Plane Strain01:12

Transformation of Plane Strain

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When analyzing elongated structures like bars subjected to uniformly distributed loads, it is essential to understand the transformation of plane strain when coordinate axes are rotated. This transformation helps to assess how material deformation characteristics vary with orientation, which is crucial in materials science and structural engineering.
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Castigliano's Theorem01:18

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Castigliano's theorem analyzes displacements and rotations in elastic structures. It relates the derivative of elastic strain energy to the applied forces or moments, allowing for the calculation of deformations. The theorem states that the partial derivative of the total strain energy of a system with respect to a specific load results in the displacement at the point where the load is applied. This principle applies to both forces and moments.
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In situ Grazing Incidence Small Angle X-ray Scattering on Roll-To-Roll Coating of Organic Solar Cells with Laboratory X-ray Instrumentation
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Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Andrew H Van Benschoten1, Pavel V Afonine2, Thomas C Terwilliger3

  • 1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.

Acta Crystallographica. Section D, Biological Crystallography
|August 8, 2015
PubMed
Summary
This summary is machine-generated.

New software, phenix.diffuse, models diffuse X-ray scattering to better understand protein and nucleic acid motions. This tool aids in refining and validating macromolecular structures, offering insights into molecular mechanisms.

Keywords:
TLScorrelated motiondiffuse scatteringstructural ensemblestructure refinement

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Area of Science:

  • Structural Biology
  • Crystallography
  • Computational Biology

Background:

  • Macromolecular X-ray crystallography faces challenges in precisely identifying intramolecular motions due to limitations of Bragg diffraction.
  • Diffuse X-ray scattering offers a way to resolve ambiguities in structural models by analyzing correlated atomic displacements.

Purpose of the Study:

  • To develop and validate computational tools for modeling and analyzing diffuse X-ray scattering data.
  • To improve the precision and validation of macromolecular structures derived from crystallography.

Main Methods:

  • Development of the phenix.diffuse software tool to calculate diffuse scattering from structural ensembles.
  • Utilizing Guinier's equation for diffuse scattering calculations.
  • Application to translation-libration-screw (TLS) refinement using phenix.tls_as_xyz to generate multi-model PDB files.

Main Results:

  • phenix.diffuse successfully calculates diffuse scattering patterns from TLS-refined structures.
  • Analysis of glycerophosphodiesterase GpdQ revealed that different TLS partitioning and motion correlations produce distinct diffuse scattering maps.
  • Demonstrated the potential of diffuse X-ray scattering to refine, validate, and analyze macromolecular structures.

Conclusions:

  • Diffuse X-ray scattering, when modeled computationally, can provide crucial information about molecular motions and disorder in crystalline samples.
  • The developed tools enable quantitative agreement assessment between experimental diffuse scattering data and structural models.
  • This approach has significant implications for understanding protein and nucleic acid dynamics, molecular mechanisms, and allostery.