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Pipeline publication

[…] as a search model for the next round of Phaser, where two dimers were searched giving a solution with TFZ = 13.5 and LGG = 246. Refinement of the solution, i.e. a tetrameric model of bradavidin, resulted in an Rfactor = 0.449, Rfree = 0.482 and FOM = 0.477. This model was used then, again, as a search model in Phaser now yielding a solution with TFZ = 20.7 and LGG = 320. The model was manually edited/rebuilt using Coot and refined with Refmac5 (Rfactor = 0.420, Rfree = 0.456 and FOM = 0.546) before rebuilding the whole structure with ARP/wARP (starting from an existing model; v. 6.1.1) –, finally giving a model of bradavidin that could be finished through further cycles of refinement with Refmac5 and modification/rebuilding with Coot. Solvent atoms and other non-protein atoms were added to the model either with the automatic procedure of ARP/wARP or Coot, or manually in Coot. Few cycles of the refinement in the middle of the structure building was done also with the software suite Phenix . We could not solve the structure without the step-by-step procedure used for molecular replacement described above., The final structure of wt bradavidin was validated using the inbuilt tools of Coot , and using MolProbity of the Phenix software suite , before deposition to the Protein Data Bank , with PDB entry code 2Y32. The data collection and structure determination statistics are summarized in ., The affinity of core-bradavidin towards Brad-tag or D-biotin was measured by isothermal titration calorimetry (ITC). We also analyzed bind […]

Pipeline specifications

Software tools REFMAC5, Coot, ARP/wARP