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Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Isoxazole azepine compound.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ENV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298.15 0.1M HEPES (7.5), 26% PEG 3350, 0.2M Amm sulphate
Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.633 α = 90 b = 56.138 β = 94.22 c = 68.118 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 210 2024-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.78 45.65 99.4 0.051 0.999 13.3 6.8 41465
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 0.8 0.696
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 1.78 45.65 39069 2027 98.48 0.20696 0.2049 0.2092 0.24845 0.2444 RANDOM 39.299
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.597 r_long_range_B_other 19.491 r_dihedral_angle_3_deg 15.197 r_dihedral_angle_2_deg 8.212 r_scangle_other 7.056 r_dihedral_angle_1_deg 5.259 r_scbond_it 5.054 r_scbond_other 5.052 r_mcangle_it 4.017 r_mcbond_it 3.165
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.597 r_long_range_B_other 19.491 r_dihedral_angle_3_deg 15.197 r_dihedral_angle_2_deg 8.212 r_scangle_other 7.056 r_dihedral_angle_1_deg 5.259 r_scbond_it 5.054 r_scbond_other 5.052 r_mcangle_it 4.017 r_mcbond_it 3.165 r_angle_refined_deg 1.965 r_angle_other_deg 0.839 r_chiral_restr 0.101 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_mcbond_other r_mcangle_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 2670 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystalClear data scaling MOLREP phasing