Computational protocol: Structure of the staphylococcal enterotoxin B vaccine candidate S19 showing eliminated superantigen activity

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Protocol publication

[…] Cooled crystals were mounted and diffraction data were collected on beamline 7A at Pohang Accelerator Laboratory (PAL). Diffraction images were indexed and integrated using HKL-2000 (Otwinowski & Minor, 1997). Initial integration data were then scaled by SCALEPACK. Phaser (McCoy et al., 2007) was used for molecular replacement prior to refinement. Detailed results and diffraction data are shown in Table 3. The data were initially indexed in a tetragonal lattice; however, they were re-indexed in an orthorhombic lattice since there was an NCS rotation parallel to the symmetry axis. [...] The refinement process was performed using PHENIX (Adams et al., 2010) and Coot (Emsley & Cowtan, 2004). The refinement statistics of S19 are given in Table 4. […]

Pipeline specifications

Software tools HKL-2000, PHENIX, Coot
Application Protein structure analysis
Chemicals Hydrogen