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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 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.79 α = 90 b = 76.43 β = 90 c = 149.06 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 2.9 41.66 99.8 0.403 0.409 0.995 12.81 37.6 11149 41.2
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 2.9 2.98 99.8 2.375 2.421 0.772 1.89 26.9
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 2.9 41.66 11149 1114 99.749 0.204 0.1977 0.2019 0.2557 0.2532 Random selection 46.905
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] 2.786 1.956 -4.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.238 r_dihedral_angle_6_deg 13.972 r_lrange_it 8.855 r_lrange_other 8.853 r_dihedral_angle_1_deg 7.192 r_scangle_it 6.567 r_scangle_other 6.565 r_dihedral_angle_2_deg 6.534 r_mcangle_other 6.178 r_mcangle_it 6.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.238 r_dihedral_angle_6_deg 13.972 r_lrange_it 8.855 r_lrange_other 8.853 r_dihedral_angle_1_deg 7.192 r_scangle_it 6.567 r_scangle_other 6.565 r_dihedral_angle_2_deg 6.534 r_mcangle_other 6.178 r_mcangle_it 6.177 r_scbond_it 4.125 r_scbond_other 4.124 r_mcbond_it 3.826 r_mcbond_other 3.823 r_angle_refined_deg 1.481 r_chiral_restr_other 1.303 r_angle_other_deg 0.66 r_nbd_other 0.227 r_nbd_refined 0.209 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_1 0.087 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.066 r_ncsr_local_group_2 0.013 r_ncsr_local_group_3 0.009 r_gen_planes_refined 0.007 r_bond_refined_d 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 3222 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 97
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling Coot model building PHASER phasing REFMAC refinement