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Catalytic domain of human tankyrase 2 in complex with benzamide adenine dinucleotide (BAD)
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 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.86 α = 90 b = 76.61 β = 90 c = 148.91 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 EIGER2 XE 16M 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 2.3 74.455 99.9 0.348 0.352 0.998 13.29 40.3 22048 38.2
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 2.3 2.36 100 1.988 2.014 0.837 2.05 39.8
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 2.3 74.455 22048 2204 99.873 0.206 0.2023 0.2089 0.2413 0.2426 Random selection 42.687
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] 1.917 1.086 -3.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.472 r_dihedral_angle_3_deg 12.112 r_lrange_other 10.559 r_lrange_it 10.553 r_dihedral_angle_2_deg 7.781 r_scangle_it 7.526 r_scangle_other 7.525 r_dihedral_angle_1_deg 6.662 r_mcangle_it 5.721 r_mcangle_other 5.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.472 r_dihedral_angle_3_deg 12.112 r_lrange_other 10.559 r_lrange_it 10.553 r_dihedral_angle_2_deg 7.781 r_scangle_it 7.526 r_scangle_other 7.525 r_dihedral_angle_1_deg 6.662 r_mcangle_it 5.721 r_mcangle_other 5.712 r_scbond_it 4.665 r_scbond_other 4.663 r_mcbond_it 3.586 r_mcbond_other 3.574 r_angle_refined_deg 1.459 r_angle_other_deg 0.521 r_nbd_other 0.284 r_dihedral_angle_other_2_deg 0.255 r_nbd_refined 0.204 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.122 r_ncsr_local_group_2 0.103 r_symmetry_xyhbond_nbd_refined 0.087 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_ncsr_local_group_1 0.056 r_ncsr_local_group_3 0.019 r_bond_refined_d 0.006 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 3250 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling Coot model building PHASER phasing