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Structure of the BRD9 bromodomain and compound 27
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% PEG3350,10% ethylene glycol, 0.1M bis-tris-propane pH 7.5, 0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.888 α = 90 b = 41.67 β = 102.58 c = 30.19 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 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) 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 1.2 53.14 94.7 0.038 0.046 0.025 0.995 17.3 3.1 39068
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 1.2 1.22 92.3 0.125 0.158 0.094 0.966 2.6
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 5MQ1 1.2 53.14 37142 1925 94.41 0.1234 0.1216 0.1214 0.158 0.1575 RANDOM 14.802
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] -0.63 -0.41 0.1 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_sphericity_free 30.028 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 15.407 r_sphericity_bonded 9.638 r_dihedral_angle_1_deg 5.336 r_rigid_bond_restr 3.188 r_angle_refined_deg 2.518 r_angle_other_deg 1.355 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_sphericity_free 30.028 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 15.407 r_sphericity_bonded 9.638 r_dihedral_angle_1_deg 5.336 r_rigid_bond_restr 3.188 r_angle_refined_deg 2.518 r_angle_other_deg 1.355 r_chiral_restr 0.146 r_bond_refined_d 0.033 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 925 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 44
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction