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X-ray Crystallography

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...

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Bayesian machine learning improves single-wavelength anomalous diffraction phasing.

Maria Jose Garcia-Bonete¹, Gergely Katona¹

¹Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, 40530, Sweden.

Acta Crystallographica. Section A, Foundations and Advances

|November 7, 2019

Summary

This summary is machine-generated.

Accurate anomalous differences are key for X-ray crystallography phasing. A multivariate Bayesian model improved phasing by analyzing correlations in Friedel

Keywords:

Bayesian inference Bijvoet pairs Friedel pairs SAD continuous rotation data collection inverse-beam geometry single-wavelength X-ray anomalous diffraction survivin

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Area of Science:

Crystallography
Structural Biology
Biophysics

Background:

Single-wavelength X-ray anomalous diffraction (SAD) is vital for solving the phase problem in X-ray crystallography.
Accurate anomalous differences are critical for determining correct crystallographic phases.

Purpose of the Study:

To evaluate the correlation of Friedel's reflection pairs after scaling using continuous rotation (CR) and inverse-beam geometry (IBG) data collection methods.
To test a multivariate Bayesian model for estimating anomalous differences, considering intensity observation correlations and positivity priors.

Main Methods:

Collected anomalous diffraction data using CR and IBG methods on lysozyme and survivin crystals.
Applied a multivariate Bayesian model to estimate anomalous differences from intensity observations.
Compared Friedel's pair correlation with an alternative Bijvoet pair method.

Main Results:

CR and IBG methods showed positive correlation between I(+) and I(-) observations, suggesting anomalous differences dominate over radiation damage.
The multivariate Bayesian model, when applied to Friedel's pairs, improved initial phasing for both crystal systems and data collection methods.
An alternative pairing method using near-simultaneous Bijvoet pairs showed lower correlation and was unsuccessful.

Conclusions:

The multivariate Bayesian model effectively utilizes correlations in Friedel's pairs for improved anomalous difference estimation in SAD phasing.
CR and IBG data collection strategies are suitable for SAD experiments when analyzed with appropriate statistical models.
Accurate phasing in X-ray crystallography relies on precise anomalous difference determination, which can be enhanced by advanced modeling techniques.