Computational protocol: Crystal structure of Gib2, a signal-transducing protein scaffold associated with ribosomes in Cryptococcus neoformans

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Protocol publication

[…] Diffraction data were collected on the PXI beamline at the Swiss Light Source (SLS) at a 1-Å wavelength using a Pilatus 6 M detector (Dectris, Switzerland) at 100 K. The data were processed using X-ray Detector Software (XDS). The structure was solved by molecular replacement with Phaser using the structure of S. cerevisiae Asc1 (PDB ID: 3FRX, Ref. ) as the search model. Subsequently, aromatic model building was carried out by ARP/wARP. The model was further improved by iterations of manual model building with COOT and refinement with Phenix. Ramachandran plot statistics were as follows: favoured (94.2%), allowed (5.2%), and outliers (0.6%). Crystallographic data and refinement are summarised in . All of the structural figures were created using MacPyMOL (www.pymol.org). […]

Pipeline specifications

Software tools XDS, ARP/wARP, Coot, PHENIX, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Cryptococcus neoformans