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First bromodomain of BRD4 in complex with ISOX-DUAL based inhibitor 30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P9H
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, 2 mM inhibitor 30.
Crystallization condition: 25% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2 38.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.997 α = 90 b = 50.706 β = 90 c = 59.715 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 2021-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 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 1.61 39 100 0.041 1 20.9 6.4 15948 25.2212795897
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 1.61 1.64 0.786 0.841 2.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.61 38.7 1.34687971121 15891 802 99.8554731683 0.173608159233 0.171390511026 0.215108203616 0.2243 5 31.7731840058
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 13.2169444555 f_angle_d 0.807560163071 f_chiral_restr 0.0424878806835 f_bond_d 0.00625485179811 f_plane_restr 0.00474288210246
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1024 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing