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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZJ12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30% PEG5000, 0.2M (NH4)2SO4, 0.1M MES monohydrate, PH6.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.73 α = 90 b = 46.81 β = 90 c = 77.38 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 193 PIXEL DECTRIS PILATUS3 6M 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 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 1.82 40.05 99.9 0.09 0.096 0.034 0.997 13.9 8.1 12201
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 1.82 1.86 99.9 0.192 0.205 0.07 0.99 8.5
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 5Z1S 1.82 40.05 11511 601 99.49 0.195 0.1917 0.259 0.2653 RANDOM 22.55
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] 2.99 -1.28 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.674 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 6.617 r_angle_refined_deg 2.121 r_angle_other_deg 1.123 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.674 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 6.617 r_angle_refined_deg 2.121 r_angle_other_deg 1.123 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 29
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing