Computational protocol: An in cellulo-derived structure of PAK4 in complex with its inhibitor Inka1

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Protocol publication

[…] A 2.95-Å data set was collected at the microfocus beamline I24 of the Diamond Light Source equipped with microapertures, limiting the beam cross-sectional area to 6 × 6 μm, at wavelength of 0.9686 Å with a PILATUS3 6 M detector (DECTRIS, Baden, Switzerland) by merging the diffraction data from five isomorphous crystals. The data were processed with xia2 (ref. ) and the structure solved by molecular replacement with Phaser, using the coordinates of the catalytic domain of human PAK4 (PDB 4FIE) as the search model. The solution was then built in COOT, refined to completion using REFMAC5 (ref. ) and validated via the MolProbity web server. Structure figures were generated using PyMOL (The PyMOL Molecular Graphics System, Version 1.3 Schrödinger, LLC). The atomic coordinates and structure factors have been deposited in the Protein Data Bank (PDB 4XBU). […]

Pipeline specifications

Software tools xia2, Coot, REFMAC5, MolProbity, PyMOL
Application Protein structure analysis
Organisms Homo sapiens
Chemicals Adenosine Triphosphate