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Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW9
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 TW12 in DMSO added to give a final inhibitor concentration 1.5 mM.
Reservoir buffer: 24% PEG 3350, 0.1 M sodium formate, 15% ethylene glycol and 0.1 M bis-Tris-propane pH 7.3.
Ratio protein/reservoir solution = 2:1
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.254 α = 90 b = 44.338 β = 90 c = 78.256 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 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 1.05 78.3 100 0.084 0.998 14.3 11.6 61370 9.65991112921
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 1.05 1.07 0.69 0.896 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 1.05 39.15 1.33737477503 61260 3095 99.9396381552 0.164805061865 0.164199975376 0.1636 0.176224999275 0.1756 14.181153913
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 10.8622616378 f_angle_d 0.82195939178 f_chiral_restr 0.0741496552007 f_plane_restr 0.00545915163667 f_bond_d 0.00497251855873
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1019 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing