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Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22032
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.959 α = 90 b = 51.056 β = 90 c = 64.369 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-F 2022-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.15 51.06 88.3 0.043 0.049 0.024 0.998 19.8 3.8 7195
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 2.15 2.22 91.8 0.095 0.111 0.055 0.99 3.4
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 2.15 40 6816 364 86.41 0.19187 0.19006 0.1959 0.22743 0.2305 RANDOM 35.246
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] -1.54 3.15 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_4_deg 18.948 r_dihedral_angle_3_deg 17.199 r_long_range_B_other 5.996 r_long_range_B_refined 5.988 r_dihedral_angle_1_deg 5.239 r_scangle_other 4.623 r_mcangle_it 3.237 r_mcangle_other 3.235 r_scbond_it 2.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_4_deg 18.948 r_dihedral_angle_3_deg 17.199 r_long_range_B_other 5.996 r_long_range_B_refined 5.988 r_dihedral_angle_1_deg 5.239 r_scangle_other 4.623 r_mcangle_it 3.237 r_mcangle_other 3.235 r_scbond_it 2.799 r_scbond_other 2.796 r_mcbond_it 2.075 r_mcbond_other 2.069 r_angle_refined_deg 1.474 r_angle_other_deg 0.92 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 928 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing