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Structure of the BRD9 bromodomain and compound 15
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 0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.11 α = 90 b = 118.69 β = 90 c = 28.33 γ = 90
Symmetry Space Group P 21 21 2
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 62.86 100 0.073 0.081 0.033 0.999 12 5.9 34080
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 1.63 100 0.586 0.649 0.274 0.435 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MQ1 1.6 62.86 32338 1686 99.97 0.1959 0.1933 0.2445 0.235 RANDOM 28.47
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] 0.69 -0.53 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 21.267 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 4.591 r_angle_refined_deg 1.956 r_angle_other_deg 1.069 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 21.267 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 4.591 r_angle_refined_deg 1.956 r_angle_other_deg 1.069 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 49
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction