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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153
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 277 1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.75 67.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.846 α = 90 b = 140.846 β = 90 c = 131.832 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 193 PIXEL DECTRIS PILATUS3 6M 2021-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.83 121.98 98.6 0.101 0.112 0.046 0.997 10.6 5.5 18670
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 2.83 2.98 99.8 0.647 0.71 0.289 0.887 5.8
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 2.83 121.98 17743 909 98.38 0.1816 0.1784 0.2465 0.2207 RANDOM 71.187
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] -4.11 -2.06 -4.11 13.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.019 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.51 r_dihedral_angle_1_deg 5.731 r_angle_refined_deg 1.566 r_angle_other_deg 1.019 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.019 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.51 r_dihedral_angle_1_deg 5.731 r_angle_refined_deg 1.566 r_angle_other_deg 1.019 r_chiral_restr 0.077 r_bond_refined_d 0.012 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 2778 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 159
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing