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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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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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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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Related Experiment Video

Updated: Apr 26, 2026

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
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The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.

James M Holton1, Scott Classen, Kenneth A Frankel

  • 1Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, USA.

The FEBS Journal
|July 22, 2014
PubMed
Summary

High R-factors in macromolecular crystallography are not due to experimental error or phase bias. Instead, current models inadequately represent macromolecular flexibility and interfaces, limiting crystallographic accuracy.

Keywords:
R-factorR-valuecrystallographysimulationtheoretical

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

  • Structural biology
  • Crystallography
  • Biophysics

Background:

  • Macromolecular crystallography often shows poor agreement between observed and predicted structure factors (Rcryst/Rfree > 20%), far exceeding experimental error (Rmerge).
  • This 'R-factor gap' is absent in small-molecule crystallography, where calculated factors are typically more accurate than experimental data.

Purpose of the Study:

  • To investigate the causes of the R-factor gap in macromolecular crystallography.
  • To determine if experimental noise or phase bias limits crystallographic model accuracy.

Main Methods:

  • Simulated macromolecular diffraction patterns using MLFSOM, incorporating all known experimental errors.
  • Processed simulated data using standard crystallographic methods.
  • Compared crystallographic statistics of simulated data with real experimental data.

Main Results:

  • Simulated data produced crystallographic statistics indistinguishable from real data, except for final Rcryst and Rfree values.
  • Rcryst and Rfree for simulated data reached 3.8% and 5.5%, respectively.
  • Neither experimental error nor phase bias explained the high R-factors observed in real macromolecular data.

Conclusions:

  • The R-factor gap stems from an inadequacy in current models to represent macromolecular flexibility and the protein-solvent interface.
  • Integrating small-angle X-ray scattering, computational chemistry, and crystallography may improve macromolecular modeling.
  • Macromolecular crystallographic data holds untapped potential for nanoscale resolution.