☰ Navigation Tabs
Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.716 α = 90 b = 43.604 β = 104.34 c = 40.88 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 100 IMAGE PLATE RIGAKU RAXIS IV 2013-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.52
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.7 19.559 97.7 0.086 0.086 0.09 0.029 20.3 9.6 14841 14841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 95.2 0.337 0.337 0.115 7.4 9.4 2064
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 3HME 1.7 19.54 14086 748 97.19 0.1502 0.1482 0.1598 0.1857 0.1955 RANDOM 15.873
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] -0.23 -0.57 0.03 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 15.703 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 4.559 r_mcangle_it 3.36 r_mcbond_other 2.558 r_mcbond_it 2.557 r_angle_refined_deg 1.747 r_angle_other_deg 0.828 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 15.703 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 4.559 r_mcangle_it 3.36 r_mcbond_other 2.558 r_mcbond_it 2.557 r_angle_refined_deg 1.747 r_angle_other_deg 0.828 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 920 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 20
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction