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An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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Reducing dynamical electron scattering reveals hydrogen atoms.

Max T B Clabbers1, Tim Gruene2, Eric van Genderen2

  • 1Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

Acta Crystallographica. Section A, Foundations and Advances
|December 22, 2018
PubMed
Summary
This summary is machine-generated.

Electron diffraction of nanometre-sized crystals enables hydrogen atom positional refinement. A new computational method improves accuracy by reducing dynamical scattering effects, even for low-resolution protein data.

Keywords:
dynamical scatteringelectron diffractionhybrid pixel detectorhydrogen atomsnanocrystals

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Area of Science:

  • Crystallography
  • Materials Science
  • Structural Biology

Background:

  • Dynamical electron scattering is a major challenge in electron diffraction, complicating structure solution.
  • Reducing crystal size minimizes dynamical scattering but also decreases diffracted intensity.
  • Existing methods for modeling dynamical scattering are limited in scope.

Purpose of the Study:

  • To demonstrate hydrogen atom positional refinement using electron diffraction on nanometre-sized organic pharmaceutical crystals.
  • To introduce a computational approach to mitigate the effects of dynamical scattering.
  • To improve the accuracy of structure solutions from weak diffraction data.

Main Methods:

  • Utilizing nanometre-sized crystals of organic pharmaceuticals.
  • Employing a highly sensitive hybrid pixel detector to capture weak diffraction data.
  • Developing and applying a general likelihood-based computational method to reduce dynamical scattering effects.

Main Results:

  • Successful positional refinement of hydrogen atoms was achieved, even when ignoring dynamical scattering during refinement.
  • The computational approach significantly improved model accuracy.
  • Enhanced accuracy was observed even for protein crystal data at substantially lower resolution.

Conclusions:

  • Nanometre-sized crystals are suitable for detailed structural analysis using electron diffraction.
  • The developed computational method offers a general solution for mitigating dynamical scattering.
  • This work advances the application of electron diffraction for precise structure determination, particularly for challenging samples.