Computational protocol: Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry

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[…] F-AΔsub crystals were prepared for vitrification by replacing the drop solution with mother liquor containing increasing amounts of glycerol [10, 20 and 30%(v/v)]. Crystals were mounted and vitrified in the nitrogen cryostream at the McGill Centre for Structural Biology for initial screening and were then stored in liquid nitrogen prior to data collection at the Canadian Light Source. Diffraction data were collected on the Canadian Macromolecular Crystallography Facility (CMCF) 08ID-1 beamline using a small-gap undulator and a Rayonix MX-300 CCD detector. Data sets were integrated and scaled using iMosflm (Battye et al., 2011) and AIMLESS (Evans & Murshudov, 2013), respectively, and in parallel using HKL-2000 (Otwinowski & Minor, 1997). Data-collection and processing statistics are given in Table 3. [...] Initial structure determination of F-AΔsub in space group P41212 was carried out by rigid-body refinement of the existing F-A model (PDB entry 5es6; Reimer et al., 2016) using PHENIX (Adams et al., 2010). Electron-density maps calculated at 5 Å in CNS (Brunger, 2007) showed the presence of a second F-AΔsub molecule. Molecular replacement was then used to solve the structure in P41 with F-A as a model using PHENIX (Adams et al., 2010). The set of reflections used to calculate R free in P41 was based on the set used in P41212 and expanded to P41 using the reflection-file editor in PHENIX (Adams et al., 2010). Iterative model building and subsequent refinements were performed in Coot (Emsley et al., 2010) and PHENIX (Adams et al., 2010). Structure-solution and refinement statistics are given in Table 4. […]

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