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Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,
PH 6.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.49 α = 90 b = 47.31 β = 90 c = 77.98 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 100 CCD ADSC QUANTUM 315 2015-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97923 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 47.31 92.9 0.048 0.022 0.999 24.5 5.9 8601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 99.3 0.1 0.044 0.994 12.6 6 633
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.99 40.45 8128 437 92.84 0.16695 0.16508 0.1768 0.20084 0.2096 RANDOM 20.137
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] 3.22 -1.65 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.546 r_dihedral_angle_4_deg 14.996 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 4.642 r_long_range_B_other 4.641 r_scangle_other 2.859 r_mcangle_it 1.789 r_mcangle_other 1.787 r_scbond_it 1.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.546 r_dihedral_angle_4_deg 14.996 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 4.642 r_long_range_B_other 4.641 r_scangle_other 2.859 r_mcangle_it 1.789 r_mcangle_other 1.787 r_scbond_it 1.744 r_scbond_other 1.743 r_angle_refined_deg 1.486 r_mcbond_other 1.116 r_mcbond_it 1.115 r_angle_other_deg 1.012 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 1115 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing