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Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW22 in DMSO added to give a final inhibitor concentration 1.5 mM.
Reservoir buffer: 24% PEG 3350, 0.2 M sodium formate, 15 % ethylene glycol and 0.1 M bis-Tris-propane pH 7.9
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.031 α = 90 b = 44.432 β = 90 c = 78.766 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2017-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.70848 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.25 78.8 99.9 0.071 0.998 13.1 7.5 36807 11.4566804012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 0.49 0.884 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 3MXF 1.25 39.4 1.3364886602 36713 1803 99.9237908603 0.161022437993 0.159396659345 0.1603 0.193345671649 0.1948 16.1780030032
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.356948688 f_angle_d 0.803398034505 f_chiral_restr 0.0686325951501 f_plane_restr 0.00552992986241 f_bond_d 0.00497873069001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing