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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...
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...
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
X-ray Imaging01:24

X-ray Imaging

German physicist Wilhelm Röntgen (1845–1923) was experimenting with electrical current when he discovered that a mysterious and invisible "ray" would pass through his flesh but leave an outline of his bones on a screen coated with a metal compound. In 1895, Röntgen made the first durable record of the internal parts of a living human: an "X-ray" image (as it came to be called) of his wife’s hand. Scientists worldwide quickly began their own experiments with X-rays, and by 1900, X-ray was widely...
Super-resolution Fluorescence Microscopy01:37

Super-resolution Fluorescence Microscopy

Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been developed.

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Updated: Jun 26, 2026

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

X-ray structure determination at low resolution.

Axel T Brunger1, Byron DeLaBarre, Jason M Davies

  • 1Howard Hughes Medical Institute, Stanford University, USA. brunger@stanford.edu

Acta Crystallographica. Section D, Biological Crystallography
|January 28, 2009
PubMed
Summary
This summary is machine-generated.

This study demonstrates that refining low-resolution (3.5-4.5 Å) crystal structures using high-resolution models significantly improves accuracy. This approach is crucial for determining protein structures like ATPase p97/VCP when high-resolution data is limited.

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Area of Science:

  • Structural biology
  • Biochemistry
  • X-ray crystallography

Background:

  • Determining protein structures at resolutions of 3.5-4.5 Å presents challenges.
  • The ATPase p97/VCP protein complex has distinct domains (N-terminal, D1, D2).

Purpose of the Study:

  • To evaluate structure determination methods for low-resolution crystallographic data.
  • To improve the refinement of the ATPase p97/VCP structure using available data.

Main Methods:

  • Molecular replacement using a high-resolution N-D1 fragment structure.
  • Manual model building of the D2 domain based on homology.
  • Re-refinement of the full-length p97 structure using refined domain models.

Main Results:

  • Re-refinement of the full-length p97 model against low-resolution data yielded significant improvements.
  • Secondary structure and R values were enhanced, with free R values dropping by up to 5%.
  • The study confirmed the utility of diffraction data around 4 Å for model quality assessment.

Conclusions:

  • Refinement of low-resolution protein structures is meaningful and improves model quality.
  • Starting refinement from high-resolution crystal structures is recommended over de novo model building at low resolution.
  • This strategy enhances the structural determination of proteins like ATPase p97/VCP.