Abstract
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
Highlights
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods
We developed the Structural Biology Data Grid (SBDG) to support the need of the SBGrid community to archive and disseminate X-ray diffraction image data sets, that is, images recorded on X-ray detectors, which support published structures
More than 90% of SBGrid laboratories use X-ray crystallography in their research, and SBGrid investigators have contributed over 11,000 X-ray structures to the PDB
Summary
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. With the exception of a modest number of data storage systems dedicated to the support of individual synchrotron beamlines[3], or specific structural genomics projects[4], storage of diffraction image data sets is typically the responsibility of primary investigators Access to these original experimental data sets is dependent on the policies of individual laboratories, which vary in storage organization, institutional resources, and researcher turnover. The Worldwide Protein Data Bank[13,14] (wwPDB) has illustrated how these achievements can be realized with the collection of reduced experimental data, in the form of structure factor amplitudes Complementing this resource by preserving raw experimental data and making it available to a broad community promises a profound scientific impact in structural biology and other biomedical disciplines that face the challenges of preserving large data sets. In 2012, SBGrid prototyped a system based on Globus technology[16,17,18,19] to move diffraction data between Harvard, The Advanced Photon Source, and the Stanford Synchrotron Radiation Light source[19]
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