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Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8J PDB ENTRY 2O8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2M sodium fluoride, 0.1M Bis-Tris phosphate pH 6.0, 18% polyethylene glycol 3350 and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.674 α = 90 b = 78.074 β = 91.81 c = 72.507 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 100 IMAGE PLATE RIGAKU RAXIS HTC VeriMax HR 2009-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 50 97.1 0.044 0.044 13 5.8 67707 67707 30.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.73 67.6 0.727 0.727 1.26 2.6 2369
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 (All) 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 PDB ENTRY 2O8J 1.7 29.58 66303 1372 96.95 0.21061 0.21061 0.2095 0.2091 0.2643 0.2649 RANDOM 33.946
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] -2.52 1.75 0.03 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.579 r_dihedral_angle_4_deg 13.739 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 5.569 r_scangle_it 2.875 r_scbond_it 1.841 r_mcangle_it 1.393 r_angle_refined_deg 1.309 r_mcbond_it 0.755 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.579 r_dihedral_angle_4_deg 13.739 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 5.569 r_scangle_it 2.875 r_scbond_it 1.841 r_mcangle_it 1.393 r_angle_refined_deg 1.309 r_mcbond_it 0.755 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4190 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 136
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling