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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 7.5 277 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.88 α = 90 b = 45.56 β = 96.87 c = 47.31 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2015-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.97776
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 1.62 45.56 89 0.092 0.042 0.994 12.1 5.5 14489
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 1.62 1.64 96.9 0.31 0.141 0.96 4.7 5.6 790
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 1.62 32.7 13771 706 88.77 0.17373 0.17239 0.1798 0.20012 0.2074 RANDOM 21.73
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] -1.1 0.16 -0.27 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_4_deg 11.305 r_long_range_B_refined 6.406 r_long_range_B_other 6.234 r_dihedral_angle_1_deg 4.968 r_scangle_other 3.812 r_mcangle_it 3.097 r_mcangle_other 3.096 r_scbond_it 2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_4_deg 11.305 r_long_range_B_refined 6.406 r_long_range_B_other 6.234 r_dihedral_angle_1_deg 4.968 r_scangle_other 3.812 r_mcangle_it 3.097 r_mcangle_other 3.096 r_scbond_it 2.268 r_scbond_other 2.266 r_mcbond_other 1.827 r_mcbond_it 1.826 r_angle_refined_deg 1.478 r_angle_other_deg 1.066 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.005 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 1101 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing