Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

A public database of macromolecular diffraction experiments

09.11.2016

The reproducibility of published experimental results has recently attracted attention in many different scientific fields. The lack of availability of original primary scientific data represents a major factor contributing to reproducibility problems, however, the structural biology community has taken significant steps towards making experimental data available.

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.


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.

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 

Dr. Jonathan Agbenyega | EurekAlert!

More articles from Life Sciences:

nachricht Cells communicate in a dynamic code
19.02.2018 | California Institute of Technology

nachricht Studying mitosis' structure to understand the inside of cancer cells
19.02.2018 | Biophysical Society

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: In best circles: First integrated circuit from self-assembled polymer

For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.

In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...

Im Focus: Demonstration of a single molecule piezoelectric effect

Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale

Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...

Im Focus: Hybrid optics bring color imaging using ultrathin metalenses into focus

For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.

But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...

Im Focus: Stem cell divisions in the adult brain seen for the first time

Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.

The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...

Im Focus: Interference as a new method for cooling quantum devices

Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters

Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on High Temperature Shape Memory Alloys (HTSMAs)

15.02.2018 | Event News

Aachen DC Grid Summit 2018

13.02.2018 | Event News

How Global Climate Policy Can Learn from the Energy Transition

12.02.2018 | Event News

 
Latest News

Contacting the molecular world through graphene nanoribbons

19.02.2018 | Materials Sciences

When Proteins Shake Hands

19.02.2018 | Materials Sciences

Cells communicate in a dynamic code

19.02.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>