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Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB503
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 NB503.
Crystallization buffer: 25% PEG 3350, 0.1 M Na malonate pH 7, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.3. Vol ratio 1:2
Crystal Properties Matthews coefficient Solvent content 2.03 39.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.318 α = 90 b = 52.505 β = 90 c = 55.054 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 EIGER X 16M 2022-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 42.3 98.5 0.036 0.999 26.5 6.6 34045 13.61
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 97 0.392 0.935 4.6 6.2
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 1.25 38 1.34 33998 1779 98.18 0.1569 0.1559 0.157 0.1748 0.1747 18.48
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 4.5816 f_angle_d 0.9551 f_chiral_restr 0.0805 f_plane_restr 0.0083 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1028 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing