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Determination of Crystal Structures

Determination of Crystal Structures

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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$Microcrystallography of Protein Crystals and In Cellulo Diffraction$

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

A grid-enabled web service for low-resolution crystal structure refinement.

Daniel J O'Donovan¹, Ian Stokes-Rees, Yunsun Nam

¹Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Acta Crystallographica. Section D, Biological Crystallography

|February 22, 2012

Summary

This study introduces a web service for Deformable Elastic Network (DEN) restraints, enabling rapid structural refinement using the Open Science Grid. This accelerates complex crystallographic data analysis for structural biologists.

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Deformable Elastic Network (DEN) restraints are crucial for refining low-resolution X-ray crystallographic data.
Optimal DEN refinement demands significant computational resources, often limiting accessibility.

Purpose of the Study:

To develop a web service providing access to high-performance computing for DEN refinements.
To enable efficient parallel processing of DEN refinements on the Open Science Grid.

Main Methods:

Implementation of a user-friendly web interface within the SBGrid Science Portal.
Leveraging the Open Science Grid for parallel computation of DEN refinements.
Integration of full parameter optimization into the refinement process.

Main Results:

Drastic reduction in computation time for DEN refinements from thousands of hours to several hours.
Successful application demonstrated on the human Notch1 transcriptional complex.
Demonstrated feasibility of large-scale, computationally intensive structural refinements.

Conclusions:

The DEN web service democratizes access to advanced structural refinement tools.
Accelerated computational methods enhance the feasibility of complex structural biology studies.
Facilitates rapid analysis of crystallographic data, advancing structural biology research.