Computational protocol: Structure of the exportin Xpo4 in complex with RanGTP and the hypusine-containing translation factor eIF5A

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Protocol publication

[…] All diffraction data were collected at the beamline X10SA (Swiss Light Source, Villigen, Switzerland). All data sets were indexed, integrated and scaled with XDS (ref. ). For phasing, 56 selenium sites (out of 66) were located by SHELXD (ref. ). Initial phases were obtained by molecular replacement with PHASER (ref. ) using Ran (PDB ID 3GJX, ref. ) and eIF5A (PDB ID 3CPF, ref. ) as search models. The resulting information and position of selenium atoms were used to obtain the electron density map in AutoSol Wizard in Phenix suite. Model building was carried out with resolve and buccaneer using AutoBuild Wizard in Phenix and with COOT (ref. ). Iterative cycles of refinement using PHENIX Refine were done after each round of model building and the quality of the model was assessed with MolProbity. In the final stages, the model was refined against a native data set at a resolution of 3.2 Å to an Rwork of 21.5% and Rfree of 26.8%. The model has good stereochemistry, with 96% of the residues in the most favoured region of the Ramachandran plot and only 0.2% outliers.All figures were prepared using USCF Chimera ( […]

Pipeline specifications

Software tools XDS, SHELX, PHENIX, Buccaneer, Coot, MolProbity
Applications Small-angle scattering, Protein structure analysis
Chemicals Amino Acids