Experiences with making diffraction image data available: what metadata do we need to archive?

Abstract

Recently, the IUCr (International Union of Crystallography) initiated the formation of a Diffraction Data Deposition Working Group with the aim of developing standards for the representation of raw diffraction data associated with the publication of structural papers. Archiving of raw data serves several goals: to improve the record of science, to verify the reproducibility and to allow detailed checks of scientific data, safeguarding against fraud and to allow reanalysis with future improved techniques. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. In a recent study of the binding of cisplatin and carboplatin to histidine in lysozyme crystals under several conditions, the possible effects of the equipment and X-ray diffraction data-processing software on the occupancies and B factors of the bound Pt compounds were compared. Initially, 35.3 GB of data were transferred from Manchester to Utrecht to be processed with EVAL. A detailed description and discussion of the availability of metadata was published in a paper that was linked to a local raw data archive at Utrecht University and also mirrored at the TARDIS raw diffraction data archive in Australia. By making these raw diffraction data sets available with the article, it is possible for the diffraction community to make their own evaluation. This led to one of the authors of XDS (K. Diederichs) to re-integrate the data from crystals that supposedly solely contained bound carboplatin, resulting in the analysis of partially occupied chlorine anomalous electron densities near the Pt-binding sites and the use of several criteria to more carefully assess the diffraction resolution limit. General arguments for archiving raw data, the possibilities of doing so and the requirement of resources are discussed. The problems associated with a partially unknown experimental setup, which preferably should be available as metadata, is discussed. Current thoughts on data compression are summarized, which could be a solution especially for pixel-device data sets with fine slicing that may otherwise present an unmanageable amount of data.

Keywords: data archiving; data exchange; derived data; metadata; processed data; raw data.

Figure 1

The web page at http://rawdata.chem.uu.nl from which raw data can be downloaded as gzip-compressed tar files. A sample image is shown for each data set and also a single image file is available in the original file format. For Bruker data both the original and unwarped data can be obtained. In the former case the p4p file is needed to unwarp images. Photos of the diffractometers can be useful in unravelling their setup.

Figure 2

The two binding sites on the His15 residue of hen egg-white lysozyme (HEWL). The F _o − F _c OMIT electron-density maps are shown in green and the anomalous difference electron-density maps are shown in orange at a 3σ cutoff: 4dd7 (Tanley, Diederichs et al., 2013a ▶) processed by (a) XDS (Kabsch, 2010 ▶) and (b) EVAL (Schreurs et al., 2010 ▶).