Computational protocol: Structural Basis for Ubiquitin Recognition by Ubiquitin Binding Zinc Finger of FAAP20

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Protocol publication

[…] Diffraction data sets were collected at the beamline BL41XU in SPring-8 (Hyogo, Japan), and they were processed with the program HKL2000 [] and the CCP4 program suite []. The crystal of the FAAP20-UBZ•K63-Ub2 complex belongs to the space group P21, with unit cell dimensions of a = 59.8 Å, b = 45.9 Å, c = 172.9 Å, β = 98.1°. The complex structures were determined by molecular replacement using the program MolRep []. The crystal structure of Ub (PDB code: 1ubq) was used as the search model. The atomic model of FAAP20-UBZ was built to fit 2F o-F c electron density map using the program COOT [] with careful inspection. Refinement was carried out using the program Refmac5 [] with iterative correction and refinement of the atomic model. The final model has excellent stereochemistry with an R free value of 23.5% at 1.90 Å resolution. Data collection and refinement statistics are shown in . All molecular graphics were prepared using the program PyMOL (DeLano Scientific; http://www.pymol.org). […]

Pipeline specifications

Software tools CCP4, Molrep, Coot, REFMAC5, PyMOL
Application Protein structure analysis
Diseases Fanconi Anemia