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Catalytic domain of human tankyrase 2 in complex with a dual-site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB_00007OJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 22% (w/v) PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, 1% (v/v) DMSO, 1 mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.71 α = 90 b = 76.3 β = 90 c = 148.98 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2023-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.8 41.62 99.8 0.232 0.24 0.995 11.11 15.6 12297 42.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 99.9 1.132 1.204 0.74 1.96 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 41.62 12297 1227 99.765 0.201 0.1967 0.2019 0.2409 0.2444 Random selection 47.212
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] 2.776 1.817 -4.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.287 r_dihedral_angle_3_deg 14.16 r_lrange_it 9.572 r_lrange_other 9.571 r_dihedral_angle_1_deg 6.893 r_dihedral_angle_2_deg 6.366 r_scangle_it 6.263 r_scangle_other 6.262 r_mcangle_it 5.962 r_mcangle_other 5.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.287 r_dihedral_angle_3_deg 14.16 r_lrange_it 9.572 r_lrange_other 9.571 r_dihedral_angle_1_deg 6.893 r_dihedral_angle_2_deg 6.366 r_scangle_it 6.263 r_scangle_other 6.262 r_mcangle_it 5.962 r_mcangle_other 5.96 r_scbond_it 3.932 r_scbond_other 3.931 r_mcbond_it 3.645 r_mcbond_other 3.644 r_angle_refined_deg 1.425 r_angle_other_deg 0.557 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.209 r_nbd_other 0.207 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.115 r_symmetry_xyhbond_nbd_refined 0.114 r_ncsr_local_group_3 0.088 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_1 0.076 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.036 r_chiral_restr_other 0.027 r_bond_refined_d 0.008 r_ncsr_local_group_2 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3232 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 107
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling Coot model building PHASER phasing REFMAC refinement