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Structure of the BRD9 bromodomain and compound 2
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 EVAPORATION 6.5 277 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.02M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.139 α = 90 b = 38.38 β = 107.13 c = 60.839 γ = 90
Symmetry Space Group P 1 21 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 1.6 58.14 98.8 0.053 0.064 0.036 0.998 8.5 2.9 33726
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 1.6 1.63 98.3 0.415 0.504 0.281 0.762 2.9
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 1.6 58.14 31997 1688 98.53 0.1816 0.1797 0.1902 0.2155 0.2191 RANDOM 24.773
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] 0.58 -0.9 1.58 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.068 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 4.511 r_angle_refined_deg 1.902 r_angle_other_deg 1.057 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.068 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 4.511 r_angle_refined_deg 1.902 r_angle_other_deg 1.057 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1835 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction iMOSFLM data reduction