A public database of macromolecular diffraction experiments

Each dot forms from the constructive interference of X-rays passing through a crystal. The data can be used to examine the crystal's structure. Credit: M. Grabowski et al.

Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data via the Protein Data Bank (PDB) and similar projects, making the field one of the most reproducible in the biological sciences.

The IUCr commissioned the Diffraction Data Deposition Working Group (DDDWG) in 2011 to examine the benefits and feasibility of archiving raw diffraction images in crystallography. The 2011-2014 DDDWG triennial report made several key recommendations regarding the preservation of raw diffraction data. However, there remains no mandate for public disclosure of the original diffraction data.

The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) is part of the Big Data to Knowledge programme of the National Institutes of Health and has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. The database [Grabowski et al. (2016). Acta Cryst. D72, 1181-1193, doi:10.1107/S2059798316014716], contains at the time of writing 3070 macromolecular diffraction experiments (5983 datasets) and their corresponding partially curated metadata, accounting for around 3% of all depositions in the Protein Data Bank.

The resource is accessible at http://www.proteindiffraction.org and can be searched using various criteria via a simple, streamlined interface. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules.

Talking to a reporter about the project, team leader Wladek Minor said, “There is so much research underway that it can't all be published, and often the results of unsuccessful studies don't appear in the literature. I think the key to success is to know about unsuccessful experiments, we want to know why they fail”.

The goal of the project is to expand the IRRMC and include data sets that failed to yield X-ray structures. This could facilitate collaborative efforts to improve protein structure-determination methods and also ensure the availability of “orphan” data left behind by individual investigators and/or extinct structural genomics projects.

Media Contact

Dr. Jonathan Agbenyega
ja@iucr.org
124-434-2878

 @iucr

http://www.iucr.org 

Media Contact

Dr. Jonathan Agbenyega EurekAlert!

All latest news from the category: Life Sciences and Chemistry

Articles and reports from the Life Sciences and chemistry area deal with applied and basic research into modern biology, chemistry and human medicine.

Valuable information can be found on a range of life sciences fields including bacteriology, biochemistry, bionics, bioinformatics, biophysics, biotechnology, genetics, geobotany, human biology, marine biology, microbiology, molecular biology, cellular biology, zoology, bioinorganic chemistry, microchemistry and environmental chemistry.

Back to home

Comments (0)

Write a comment

Newest articles

When the music changes, so does the dance

Controlling cooperative electronic states in Kagome metals. Playing a different sound track is, physically speaking, only a minute change of the vibration spectrum, yet its impact on a dance floor…

EcoFABs could lead to better bioenergy crops

Fabricated ecosystems created at Berkeley Lab will expedite microbiome research, and help underrepresented students in the classroom. A greater understanding of how plants and microbes work together to store vast…

Rice lab finds better way to handle hard-to-recycle material

Process transforms glass fiber-reinforced plastic into silicon carbide. Glass fiber-reinforced plastic (GFRP), a strong and durable composite material, is widely used in everything from aircraft parts to windmill blades. Yet…

Partners & Sponsors