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Human tankyrase 2 - catalytic PARP domain in complex with an inhibitor XAV939
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 8.5 277 17% PEG 3350, 0.2M AmmoniumSulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.75 α = 90 b = 97.975 β = 90 c = 119.464 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 Bruker Platinum 135 2009-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54187
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 2.1 45 99.8 0.154 0.132 12.7 13.4 31809 31809
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 2.1 2.15 96.3 0.419 0.314 3.5 7 2104
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 2.1 44.46 29779 29779 1571 99.78 0.20131 0.20131 0.19846 0.2016 0.25492 0.2592 RANDOM 13.009
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] -0.1 -0.67 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 6.424 r_scangle_it 3.806 r_scbond_it 2.425 r_mcangle_it 1.629 r_angle_refined_deg 1.562 r_mcbond_it 0.905 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 6.424 r_scangle_it 3.806 r_scbond_it 2.425 r_mcangle_it 1.629 r_angle_refined_deg 1.562 r_mcbond_it 0.905 r_angle_other_deg 0.885 r_mcbond_other 0.226 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 3322 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 76
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement SAINT data reduction SAINT data scaling