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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.
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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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A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.

Helen Mary Ginn1, Aaron S Brewster2, Johan Hattne2

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Acta Crystallographica. Section D, Biological Crystallography
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Summary
This summary is machine-generated.

Improved X-ray diffraction models for X-ray free-electron laser (XFEL) data enable more reliable structure determination using sulfur single-wavelength anomalous dispersion (SAD) phasing. This advance enhances XFEL utility for challenging biological systems.

Keywords:
free-electron laserpartialitypost-refinement

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Area of Science:

  • Structural Biology
  • Crystallography
  • Biophysics

Background:

  • X-ray free-electron laser (XFEL) data are crucial for solving biological structures.
  • Current diffraction models for XFEL data have limitations, hindering experimental phasing methods like sulfur single-wavelength anomalous dispersion (SAD).
  • Errors in orientation matrices and partiality models necessitate large image datasets for accurate structure-factor amplitude estimation.

Purpose of the Study:

  • To refine existing partiality models for X-ray diffraction data from XFELs.
  • To improve the accuracy of structure-factor amplitudes derived from XFEL datasets.
  • To enhance the feasibility of sulfur SAD phasing for biological structure determination using XFELs.

Main Methods:

  • Revisiting cytoplasmic polyhedrosis virus type 17 (CPV17) data collected at the Linac Coherent Light Source (LCLS).
  • Building upon a published partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses.
  • Implementing a post-refinement method to refine model parameters using a super-Gaussian wavelength distribution.

Main Results:

  • A refined merged dataset with an R(split) value of 3.15% to 1.46 Å resolution was generated from 7225 images.
  • Atomic numbers of C, N, and O atoms were distinguishable in the electron-density map.
  • Sulfur atoms, despite low anomalous scattering, were detectable in the anomalous difference Fourier map.

Conclusions:

  • The improved diffraction models enhance the utility of XFEL data for structural studies.
  • This work facilitates XFEL experimental phase determination and structure determination by sulfur SAD.
  • The refined methods are particularly beneficial for analyzing difficult biological systems with limited data.