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Human tankyrase 2 - catalytic PARP domain in complex with 1-methyl-3-(trifluoromethyl)-5h-benzo[c][1,8]naphtyridine-6-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KR7 PDB ENTRY 3KR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 17% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.547 α = 90 b = 97.727 β = 90 c = 119.126 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r liquid nitrogen cooled channel-cut silicon monochromator and cylindrical grazing incidence mirror 2009-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 ESRF ID29
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 1.8 45.21 99.9 0.054 0.057 24.6 7.1 49107 49107
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 1.8 1.85 99.8 0.452 0.429 3.7 5 3582
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3KR7 1.8 45.21 46650 46650 2456 100 0.17296 0.17296 0.17137 0.1748 0.20275 0.205 RANDOM 18.601
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] -0.29 -0.45 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.102 r_dihedral_angle_4_deg 18.346 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_1_deg 6.544 r_scangle_it 4.624 r_scbond_it 2.851 r_mcangle_it 2.012 r_angle_refined_deg 1.624 r_mcbond_it 1.106 r_angle_other_deg 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.102 r_dihedral_angle_4_deg 18.346 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_1_deg 6.544 r_scangle_it 4.624 r_scbond_it 2.851 r_mcangle_it 2.012 r_angle_refined_deg 1.624 r_mcbond_it 1.106 r_angle_other_deg 0.887 r_mcbond_other 0.3 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3315 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 57
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling