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Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1181-1193. Epub 2016 Oct 28.

A public database of macromolecular diffraction experiments.

Author information

1
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA.
2
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 90237, USA.
3
RCSB Protein Data Bank; Center for Integrative Proteomics Research; Institute for Quantitative Biomedicine; Rutgers Cancer Institute of New Jersey; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Abstract

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. 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. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

KEYWORDS:

IRRMC; data; diffraction experiment; metadata; protein crystallography; repository

PMID:
27841751
PMCID:
PMC5108346
DOI:
10.1107/S2059798316014716
[Indexed for MEDLINE]
Free PMC Article

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