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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...
Nuclear Overhauser Enhancement (NOE)01:06

Nuclear Overhauser Enhancement (NOE)

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. This phenomenon, called the nuclear Overhauser enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active...
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...
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...
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...

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Related Experiment Video

Updated: Jun 7, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Joint X-ray and neutron refinement with phenix.refine.

Pavel V Afonine1, Marat Mustyakimov, Ralf W Grosse-Kunstleve

  • 1Lawrence Berkeley National Laboratory, Physical Biosciences Division, MS 64R0121, CA 94720, USA. pafonine@lbl.gov

Acta Crystallographica. Section D, Biological Crystallography
|November 3, 2010
PubMed
Summary

Neutron crystallography is crucial for determining hydrogen atom positions in biological macromolecules, complementing X-ray crystallography. This study details methods for refining structures using both X-ray and neutron data in the PHENIX system.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Crystallography

Background:

  • X-ray crystallography is the primary method for macromolecular structure determination, accounting for 85% of Protein Data Bank entries.
  • A key limitation of X-ray crystallography is the inability to directly resolve hydrogen atom positions, which are critical in active sites.
  • Hydrogen atoms play vital roles in the mechanisms of biological macromolecules.

Purpose of the Study:

  • To describe the implementation of structure-refinement procedures that integrate both X-ray and neutron diffraction data.
  • To enhance the accuracy of macromolecular structure determination by including hydrogen atom positions.
  • To leverage the complementary strengths of X-ray and neutron crystallography for complete structural analysis.

Main Methods:

  • Utilizing the PHENIX software system for crystallographic structure refinement.
  • Implementing procedures that can incorporate X-ray data, neutron data, or a combination of both.
  • Analyzing experimental neutron scattering density maps for direct hydrogen atom localization.

Main Results:

  • Demonstrated the capability of PHENIX to refine structures using both X-ray and neutron data.
  • Enabled the precise determination of hydrogen atom positions, particularly in biologically significant regions.
  • Facilitated the derivation of complete macromolecular structures by combining X-ray and neutron datasets.

Conclusions:

  • The integration of X-ray and neutron crystallography data in PHENIX provides a powerful approach for high-resolution structural analysis.
  • Accurate hydrogen atom placement is essential for understanding enzymatic mechanisms and biological function.
  • This combined approach advances the field of structural biology by overcoming limitations of individual techniques.