Computational protocol: SAD phasing using iodide ions in a high-throughput structural genomics environment

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Protocol publication

[…] Data sets were collected in house using either a Rigaku 007-HF or Rigaku SuperBright FR-E+ X-ray generator with Osmic VariMax HF optics and a Saturn 944 or Saturn 944+ CCD detector. Diffraction images are available through the CSGID web page (www.csgid.org). Data were reduced with XDS/XSCALE [] with the Bijvoet pairs unmerged (i.e., Friedel setting at FALSE). Sites were located using either phenix.hyss/phenix.autosol [] or SHELXD []. The anomalous substructure was refined and extended, and phases were estimated using PHASER EP [] from the CCP4 suite [] followed by density improvement in PARROT []. Initial models were built using automated building in BUCCANEER [], followed by model extension/rebuilding in ARP/wARP []. The model was refined using SAD refinement with optimization of the iodide ion occupancy in REFMAC []. Final models were produced after numerous iterative rounds of manual re-building in Coot [] and refinement in REFMAC [] using the merged data (i.e., Friedel setting at TRUE in XSCALE []). The correctness of each structure was examined, validated, and improved using Molprobity [, ]. […]

Pipeline specifications

Software tools XDS, PHENIX, SHELX, CCP4, Buccaneer, ARP/wARP, Coot, MolProbity
Applications Small-angle scattering, Protein structure analysis
Diseases Communicable Diseases