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Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB462
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YQN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB462. Crystallization buffer: 24% PEG 3350, 0.15 M Na formate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.6. Vol. ratio 1:2
Crystal Properties Matthews coefficient Solvent content 2.02 39.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.685 α = 90 b = 51.485 β = 91.016 c = 53.112 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2021-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.23 44.7 97.6 0.072 0.991 8.8 4.9 68247 15.12
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 1.23 1.25 95.4 0.781 0.835 2.3 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT FREE R-VALUE 1.23 44.68 1.35 68224 3277 97.5 0.168 0.1667 0.167 0.1933 0.1931 20.08
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 5.8744 f_angle_d 0.9711 f_chiral_restr 0.076 f_plane_restr 0.0077 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2031 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing