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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 2.0 M Sodium formate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.8 67.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.409 α = 90 b = 140.409 β = 90 c = 134.482 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2023-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.78 134.48 97 0.224 0.232 0.058 0.996 9 15.6 19675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.93 100 1.289 1.337 0.349 0.858 14.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7wjs 2.78 121.6 18692 939 96.95 0.18797 0.18576 0.1929 0.2336 0.236 RANDOM 63.77
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] -3.15 -1.58 -3.15 10.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.802 r_dihedral_angle_3_deg 20.137 r_dihedral_angle_4_deg 13.148 r_long_range_B_refined 11.307 r_long_range_B_other 11.307 r_scangle_other 8.681 r_mcangle_other 7.879 r_mcangle_it 7.878 r_dihedral_angle_1_deg 6.115 r_scbond_it 5.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.802 r_dihedral_angle_3_deg 20.137 r_dihedral_angle_4_deg 13.148 r_long_range_B_refined 11.307 r_long_range_B_other 11.307 r_scangle_other 8.681 r_mcangle_other 7.879 r_mcangle_it 7.878 r_dihedral_angle_1_deg 6.115 r_scbond_it 5.427 r_scbond_other 5.426 r_mcbond_it 5.127 r_mcbond_other 5.126 r_angle_refined_deg 1.978 r_angle_other_deg 1.19 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing