Computational protocol: Distributed structure determination at the JCSG

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Protocol publication

[…] Xsolve implements all processing steps required to compute an electron-density map and a trace from diffraction images. It executes well established third-party software programs for data reduction (indexing, integration and scaling), phasing and tracing of the experimental maps in succession without human intervention. The third-party software programs currently included are MOSFLM (Leslie, 1992), XDS (Kabsch, 2010) and HKL-2000 (Otwinowski & Minor, 1997; for testing only) for data reduction; SHELXD (Sheldrick, 2008), SOLVE (Terwilliger & Berendzen, 1999) and autoSHARP (Vonrhein et al., 2007) for heavy-atom location and phasing; and ARP/wARP (Perrakis et al., 1999), RESOLVE (Terwilliger, 2003) and Buccaneer (Cowtan, 2006) for building a model into the electron-density map. Fig. 1 depicts the flow of information in Xsolve. Xsolve can also solve a data set using molecular replacement (MR). A protocol similar to that reported in Schwarzenbacher et al. (2008) was implemented. Parameters such as multiple MR templates, resolution cutoff and space groups are explored in parallel using multiple MR programs: MOLREP (Vagin & Teplyakov, 2010), EPMR (Kissinger et al., 1999) and Phaser (Storoni et al., 2004). Potential MR solutions are subjected to rigid-body refinement and restrained refinement with REFMAC (Murshudov et al., 1997). Model rebuilding is carried out using ARP/wARP and RESOLVE. As the JCSG uses single-wavelength or multiwavelength anomalous diffraction (SAD/MAD) techniques to obtain phases for the vast majority of its targets, the remainder of this paper will focus on SAD/MAD data.Once a data set has been collected, a crystallographer completes a simple web form to inform the system of a few parameters, such as the location of the diffraction images, the resolution limit and theoretical or experimentally determined anomalous scattering factors. Optionally, to limit the search space, space groups and the number of monomers in the asymmetric unit can be provided as input to Xsolve. The data-collection strategy is reconstructed from parsing diffraction-image headers. Additional parameters, such as the amino-acid sequence, molecular weight and heavy-atom information, are automatically read from a database. The molecular weight can also trivially be derived from the sequence. Once this is complete, the job can be submitted to Xsolve with a different web form. The status of Xsolve can also be checked within a browser. Screenshots of the three web forms are included as supplementary material to this paper. […]

Pipeline specifications

Software tools HKL-2000, SHELX, ARP/wARP, Buccaneer, Molrep
Application Protein structure analysis
Organisms Homo sapiens