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Human tankyrase 2 - catalytic PARP domain in complex with 2-(2-pyridyl)-7,8-dihydro-5h-thiino[4,3-d]pyrimidin-4-ol
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 1.34M dipotassium hydrogen phosphate, 0.06M sodium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.484 α = 90 b = 92.484 β = 90 c = 53.506 γ = 120
Symmetry Space Group P 31 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 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 2.3 46.24 99.1 0.097 0.065 22.2 10.9 11932 11932
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 2.3 2.36 97.8 0.557 0.287 5.9 10.5 880
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 2.3 46.24 11335 11335 597 100 0.17948 0.17948 0.17691 0.178 0.22725 0.2284 RANDOM 17.789
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] 0.35 0.18 0.35 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_4_deg 13.706 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.254 r_scbond_it 1.969 r_mcangle_it 1.353 r_angle_refined_deg 1.308 r_angle_other_deg 0.808 r_mcbond_it 0.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_4_deg 13.706 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.254 r_scbond_it 1.969 r_mcangle_it 1.353 r_angle_refined_deg 1.308 r_angle_other_deg 0.808 r_mcbond_it 0.687 r_mcbond_other 0.127 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 1686 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 36
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling