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Tankyrase 2 in complex with two small molecule fragments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 100mM Tris pH=8.5, 200 mM Li2SO4, 24% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.645 α = 90 b = 76.386 β = 90 c = 148.875 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 2M 2020-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 148.88 99.9 0.981 5.9 24.4 21934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.728
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NOB 2.3 74.549 21873 1107 99.963 0.234 0.232 0.2418 0.2769 0.2858 15.737
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] 3.27 0.273 -3.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.583 r_dihedral_angle_4_deg 17.25 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 6.75 r_lrange_it 3.754 r_lrange_other 3.718 r_mcangle_it 2.083 r_mcangle_other 2.082 r_angle_refined_deg 1.198 r_scangle_it 1.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.583 r_dihedral_angle_4_deg 17.25 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 6.75 r_lrange_it 3.754 r_lrange_other 3.718 r_mcangle_it 2.083 r_mcangle_other 2.082 r_angle_refined_deg 1.198 r_scangle_it 1.185 r_scangle_other 1.182 r_mcbond_it 1.102 r_mcbond_other 1.102 r_angle_other_deg 1.098 r_scbond_it 0.614 r_scbond_other 0.597 r_nbd_other 0.221 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.171 r_symmetry_nbd_refined 0.162 r_nbd_refined 0.16 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.132 r_ncsr_local_group_1 0.079 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.042 r_metal_ion_refined 0.012 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3227 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing