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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...
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...
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...

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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals.

Oleg Mikhailovskii1, Sergei A Izmailov1, Yi Xue2,3

  • 1Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia.

Journal of Chemical Information and Modeling
|December 26, 2023
PubMed
Summary
This summary is machine-generated.

Amber 2023 introduces a new crystallography module, "xray," enhancing protein structure refinement. This tool accelerates the process, improving crystallographic model accuracy and scores.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Molecular dynamics (MD) simulations refine protein crystallographic structures.
  • Amber's force fields regularize coordinates and reconstruct flexible loops.
  • Restrained MD simulations optimize crystal models with solvent and contacts.

Purpose of the Study:

  • Introduce the new crystallography module 'xray' in Amber 2023.
  • Enable efficient and GPU-accelerated refinement of protein crystal structures.
  • Improve crystallographic model quality and accuracy.

Main Methods:

  • Developed the 'xray' module within the Amber 2023 package.
  • Implemented functions for structure factor calculation, scaling, and crystallographic potential evaluation.
  • Utilized GPU acceleration for rapid refinement of numerous crystal models, including supercells.

Main Results:

  • Achieved significant improvements in R-factors (up to 0.067).
  • Enhanced MolProbity scores, indicating better model quality.
  • Enabled refinement of hundreds of crystal models in a short time.

Conclusions:

  • The 'xray' module in Amber 2023 provides a powerful, efficient platform for protein structure refinement.
  • GPU acceleration and streamlined calculations lead to improved crystallographic model accuracy.
  • This advancement facilitates more precise determination of protein structures.