Computational protocol: Design and Characterization of Bivalent BET Inhibitors

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Protocol publication

[…] A half equivalence of MT1 (10 mM in DMSO) was mixed with 500 µM protein and crystallized by sitting-drop vapor diffusion at 20 °C in the following crystallization buffer: 2 M NH4SO4 and 0.1 M BisTris pH 5.5. Crystals were transferred briefly into crystallization buffer containing 25% glycerol prior to flash-freezing in liquid nitrogen. Diffraction data from complex crystals were collected at beamline 24ID-E of the NE-CAT at the Advanced Photon Source (Argonne National Laboratory). Data sets were integrated and scaled using XDS. Structures were solved by molecular replacement using the program Phaser and the search model PDB entry 3MXF. The ligand was positioned and preliminarily refined using Buster and Rhofit. Iterative manual model building and refinement using Phenix and Coot led to a model with excellent statistics,. The solved structure has been submitted to the PDB as 5JWM. […]

Pipeline specifications

Software tools XDS, PHENIX, Coot
Applications Small-angle scattering, Protein structure analysis
Organisms Mus musculus
Diseases Leukemia