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Crystal structure of the BRD7 bromodomain in complex with BI-9564
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other BRD9 in complex with TB-472
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 20% PEG6000, 10%EDO, 0.1 M HEPES pH 7.0, 0.01 M ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.87 α = 90 b = 125.255 β = 90 c = 37.353 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2016-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 35.42 99.7 10.4 6.6 25529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 2.1 6.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BRD9 in complex with TB-472 1.5 35.42 24238 1286 99.59 0.16337 0.16191 0.1617 0.19033 0.1912 RANDOM 13.488
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] 0.39 -0.6 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.557 r_dihedral_angle_3_deg 15.037 r_long_range_B_refined 6.063 r_long_range_B_other 5.514 r_dihedral_angle_4_deg 5.229 r_dihedral_angle_1_deg 4.973 r_scangle_other 2.299 r_angle_refined_deg 1.942 r_mcangle_it 1.822 r_mcangle_other 1.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.557 r_dihedral_angle_3_deg 15.037 r_long_range_B_refined 6.063 r_long_range_B_other 5.514 r_dihedral_angle_4_deg 5.229 r_dihedral_angle_1_deg 4.973 r_scangle_other 2.299 r_angle_refined_deg 1.942 r_mcangle_it 1.822 r_mcangle_other 1.821 r_scbond_it 1.575 r_scbond_other 1.545 r_angle_other_deg 1.116 r_mcbond_it 1.058 r_mcbond_other 1.054 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 880 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing