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Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Mivebresib ABBV-075
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1M Hepes (7.5),
26% PEG 3350,
0.2M Amm sulphate
Crystal Properties Matthews coefficient Solvent content 2.84 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.7 α = 90 b = 55.96 β = 95.53 c = 69.33 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 100 CCD Bruker AXIOM 200 2025-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5678
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 2.3 56.59 99.9 0.097 0.972 9.3 3.1 19465
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 2.3 2.39 0.261 0.545
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 2.3 56.59 18517 947 99.9 0.21513 0.21157 0.2213 0.28403 0.27 RANDOM 19.815
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] -0.1 -0.07 -0.05 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.429 r_long_range_B_refined 13.371 r_long_range_B_other 13.37 r_dihedral_angle_2_deg 8.079 r_dihedral_angle_1_deg 6.627 r_scangle_other 3.674 r_mcangle_it 2.786 r_angle_other_deg 2.307 r_scbond_it 2.251 r_scbond_other 2.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.429 r_long_range_B_refined 13.371 r_long_range_B_other 13.37 r_dihedral_angle_2_deg 8.079 r_dihedral_angle_1_deg 6.627 r_scangle_other 3.674 r_mcangle_it 2.786 r_angle_other_deg 2.307 r_scbond_it 2.251 r_scbond_other 2.251 r_angle_refined_deg 1.738 r_mcbond_it 1.703 r_chiral_restr 0.12 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 2685 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing