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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...

$X-ray Diffraction of Biological Samples$ 01:10

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...

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Related Experiment Video

Updated: Oct 13, 2025

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

Optimal structure determination from sub-optimal diffraction data.

Wladek Minor¹, Marcin Cymborowski¹, Dominika Borek^2,3

¹Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.

Protein Science : a Publication of the Protein Society

|November 16, 2021

Summary

This summary is machine-generated.

The HKL-3000 system streamlines macromolecular structure determination, accelerating the process and improving success rates, especially for challenging X-ray diffraction data. This updated software is crucial for high-quality structural biology research.

Keywords:

high-quality macromolecular structures macromolecular structure determination optimal structure determination

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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

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Last Updated: Oct 13, 2025

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

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Area of Science:

Structural Biology
Crystallography
Biophysics

Background:

The HKL family of programs has been instrumental in macromolecular structure determination, contributing to nearly 50% of X-ray diffraction-based structures in the Protein Data Bank (PDB).
Previous versions, HKL and HKL-2000, laid the foundation for automated structure solution pipelines.

Purpose of the Study:

To introduce the latest version of the HKL-3000 system, enhancing its capabilities for macromolecular structure determination.
To optimize the system's heuristics for selecting optimal approaches across all structure determination steps, accommodating diverse sample and data qualities.
To improve the success rate of structure determination, particularly for challenging datasets.

Main Methods:

Integration of data collection, data reduction, phasing, model building, refinement, and validation within a single system.
Optimization of algorithms and heuristics for automated decision-making in structure determination workflows.
Development and implementation of advanced algorithms to handle difficult diffraction data.

Main Results:

The newest HKL-3000 system significantly accelerates the structure determination process.
The system demonstrates high value in determining very high-quality macromolecular structures.
Optimized heuristics enhance the likelihood of successful structure determination, even with challenging data.

Conclusions:

The HKL-3000 system represents a significant advancement in automated macromolecular structure determination.
Its integrated approach and optimized algorithms provide a powerful tool for structural biologists.
The system is expected to further contribute to the growing body of structural data, aiding in biological research.