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Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13195
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 277 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.77 67.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.99 α = 90 b = 140.99 β = 90 c = 132.27 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 PILATUS3 6M 2023-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
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 2.79 37.41 100 0.129 0.132 0.027 1 20 22.4 19901
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 2.79 2.94 100 2.819 2.881 0.59 0.762 23.4
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 2.79 37.41 18887 976 99.91 0.2044 0.20247 0.2089 0.24354 0.2432 RANDOM 93.594
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] -5.22 -2.61 -5.22 16.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.495 r_dihedral_angle_3_deg 18.252 r_long_range_B_refined 12.503 r_long_range_B_other 12.501 r_dihedral_angle_4_deg 10.096 r_scangle_other 9.861 r_mcangle_it 9.032 r_mcangle_other 9.032 r_scbond_it 6.528 r_scbond_other 6.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.495 r_dihedral_angle_3_deg 18.252 r_long_range_B_refined 12.503 r_long_range_B_other 12.501 r_dihedral_angle_4_deg 10.096 r_scangle_other 9.861 r_mcangle_it 9.032 r_mcangle_other 9.032 r_scbond_it 6.528 r_scbond_other 6.365 r_mcbond_it 5.929 r_mcbond_other 5.909 r_dihedral_angle_1_deg 5.802 r_angle_refined_deg 1.398 r_angle_other_deg 1.124 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2736 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing