Computational protocol: Structural Basis of Rnd1 Binding to Plexin Rho GTPase Binding Domains (RBDs)*

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[…] Diffraction data were collected at beam line 19-ID at the Advanced Photon Source (Argonne, IL) with a Quantum-315 CCD detector (ADSC) and reduced with the HKL3000 suite (). The structure of the plexin-A2 RBD·Rnd1 complex was solved by molecular replacement with MOLREP () using models of Rnd1 (PDB code 2REX) () and murine plexin-A3 RBD (PDB code 3IG3) () as starting models. Initial phases for the plexin-D1 structure were obtained by single-wavelength anomalous diffraction, using the programs SHELX (), MLPHARE (), and DM () through the HKL3000 interface. The structure of plexin-C1 was solved by molecular replacement with the program PHASER () and a composite search model of plexin-D1 (described here) and the mouse plexin-A3 RBD coordinates () (PDB code 3IG3). ARP/wARP was used for automated model building, PHENIX () and REFMAC () for coordinate/B-factor refinement, COOT () for manual model adjustments, and MOLPROBITY () for validation of geometry. […]

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