Computational protocol: Experimental phasing using zinc anomalous scattering

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Protocol publication

[…] Diffraction data were processed and scaled using DENZO and SCALEPACK from the HKL-2000 program suite (Otwinowski & Minor, 1997). Experimental phasing of CMY-10 and lysozyme was performed with the AutoSol program (Terwilliger et al., 2009) in the PHENIX suite (Adams et al., 2010), which is an experimental phasing pipeline that combines HySS (Hybrid Substructure Search; Grosse-Kunstleve & Adams, 2003) for finding heavy-atom sites, Phaser (McCoy et al., 2007) or SOLVE (Terwilliger, 2002) for calculating experimental phases and RESOLVE (Terwilliger, 2002) for density modification and model building. Experimental phasing of TON_0340 was performed with autoSHARP (Vonrhein et al., 2007), an automatic structure-solution system that includes the heavy-atom refinement and phasing program SHARP (de La Fortelle & Bricogne, 1997), the density-modification program SOLOMON (Abrahams & Leslie, 1996) and the ARP/wARP package (Perrakis et al., 1999) for automated model building and refinement. The auto-built models from the phasing programs were completed using Coot (Emsley & Cowtan, 2004) and refinement was performed with a maximum-likelihood algorithm implemented in CNS (BrĂ¼nger et al., 1998). […]

Pipeline specifications

Software tools HKL-2000, PHENIX, ARP/wARP
Application Protein structure analysis
Chemicals Zinc