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Crystal structure of TNKS2 in complex with 2-(4-(propan-2-yl)phenyl)- 1H,2H,3H,4H-pyrido(2,3-d)pyrimidin-4-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U9H PDB ENTRY 3U9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.91 α = 90 b = 96.82 β = 90 c = 116.8 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 ADSC CCD 2014-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 50 99.7 0.11 12.1 5.5 41578 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.8 0.93 1.78 5.5
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 (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 3U9H 1.9 37.27 39594 2084 99.72 0.18671 0.18503 0.1939 0.21856 0.2279 RANDOM 28.071
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] 0.36 -1.18 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.807 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.222 r_dihedral_angle_1_deg 6.153 r_mcangle_it 2.78 r_scbond_it 2.655 r_mcbond_it 1.91 r_mcbond_other 1.91 r_angle_refined_deg 1.469 r_angle_other_deg 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.807 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.222 r_dihedral_angle_1_deg 6.153 r_mcangle_it 2.78 r_scbond_it 2.655 r_mcbond_it 1.91 r_mcbond_other 1.91 r_angle_refined_deg 1.469 r_angle_other_deg 0.823 r_chiral_restr 0.105 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3347 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing