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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13157
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.8 67.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.205 α = 90 b = 141.205 β = 90 c = 132.727 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 197 PIXEL DECTRIS PILATUS3 6M 2021-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97911 SSRF BL02U1
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 2.73 44.97 99.4 0.083 0.092 0.039 0.997 12.9 5.4 21133
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 2.73 2.86 100 0.747 0.833 0.363 0.829 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6viw 2.73 44.97 20064 1045 99.11 0.1826 0.1809 0.2149 0.2139 RANDOM 79.584
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] -2.84 -1.42 -2.84 9.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_3_deg 16.891 r_dihedral_angle_4_deg 12.825 r_dihedral_angle_1_deg 5.518 r_angle_refined_deg 1.462 r_angle_other_deg 1.093 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_3_deg 16.891 r_dihedral_angle_4_deg 12.825 r_dihedral_angle_1_deg 5.518 r_angle_refined_deg 1.462 r_angle_other_deg 1.093 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2724 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 174
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing