Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

Abstract

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.

Experiences with archived raw diffraction images data: capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal

“…Subsequently, these studies have been expanded when one of us (KD) joined in the detailed further analyses of each set of raw diffraction images with XDS (Kabsch, 1988). The motivation for this collaboration was due to the title of the previously published article (Tanley et al, 2013a) which suggested that a rather comprehensive approach was taken to compare software packages, with the implicit intention to correlate some metrics of data quality [R merge , I/, CC 1/2 , completeness and diffraction precision index (DPI) values, all as a function of resolution] with the amount of biological insight that these data allow one to obtain. Thus, a comprehensive investigation becomes even more useful with every addition that broadens its basis, which suggested contributing the processing with yet another widely used software package (XDS) on the existing raw diffraction data images.…”

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data

“…This is in line with the newly adopted data policy at the ESRF and the recommendations of the International Union of Crystallography (IUCr). [67,68] Once collected, data sets will be assigned a digital object identifier, archived and embargoed for three years. This will allow data sets to be linked to publications and make a valuable resource for the community open access, once released.…”

How to make deposition of images a reality

“…However, these are tailored to very specific purposes and it is likely that other schemas would need to be designed to integrate with applications from other scientific disciplines. Example of a research publication (a) providing links (as supplementary materials) to copies of the experimental diffraction images (Tanley et al, 2013) on a server at the University to which some of the authors are affiliated (b) and mirrored within the MyTARDIS system (c). The MyTARDIS interface summarizes the number of data sets, the number of files within each, the size of the individual data sets and access rights.…”

“…TARDIS has recently been used to mirror raw data sets hosted on a University server in Europe and referenced from a published article (Tanley et al, 2013). Fig.…”