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Crystal Structure of the second bromodomain of human BRD2 BD2 in complex with the inhibitor Y13195
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 3.5 M Sodium formate, 0.1 M Sodium acetate trihydrate pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.69 66.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.27 α = 90 b = 95.53 β = 90 c = 110.71 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 80 PIXEL DECTRIS PILATUS 6M 2024-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97946 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.77 42.24 98.5 0.05 0.052 0.015 1 23.6 11.4 91270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 84.9 1.04 1.147 0.47 0.616 5.5
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 7WNI 1.77 42.24 86753 4442 98.31 0.18196 0.18108 0.1897 0.19904 0.2059 RANDOM 34.721
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] 1.87 -0.57 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.364 r_dihedral_angle_4_deg 23.533 r_dihedral_angle_3_deg 14.776 r_long_range_B_refined 6.647 r_long_range_B_other 6.586 r_scangle_other 5.129 r_dihedral_angle_1_deg 5.048 r_scbond_it 3.331 r_scbond_other 3.33 r_mcangle_it 3.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.364 r_dihedral_angle_4_deg 23.533 r_dihedral_angle_3_deg 14.776 r_long_range_B_refined 6.647 r_long_range_B_other 6.586 r_scangle_other 5.129 r_dihedral_angle_1_deg 5.048 r_scbond_it 3.331 r_scbond_other 3.33 r_mcangle_it 3.004 r_mcangle_other 3.004 r_mcbond_it 2.11 r_mcbond_other 2.109 r_angle_refined_deg 1.498 r_angle_other_deg 1.345 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3614 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing