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Crystal structure of TNKS2 in complex with 2-(2,4-dichlorophenyl)-1- methyl-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 = 90.62 α = 90 b = 98.57 β = 90 c = 118.76 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 PIXEL DECTRIS PILATUS 6M 2013-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.75 50 99.2 0.07 18 6.7 53428 -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 1.75 1.8 98.7 0.99 2.34 6.9
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 1.75 29.81 50756 2672 99.23 0.16045 0.15873 0.1678 0.19309 0.1986 RANDOM 26.239
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] 0.94 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.773 r_dihedral_angle_4_deg 14.411 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 6.043 r_scbond_it 2.723 r_mcangle_it 2.7 r_mcbond_it 1.806 r_mcbond_other 1.805 r_angle_refined_deg 1.466 r_angle_other_deg 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.773 r_dihedral_angle_4_deg 14.411 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 6.043 r_scbond_it 2.723 r_mcangle_it 2.7 r_mcbond_it 1.806 r_mcbond_other 1.805 r_angle_refined_deg 1.466 r_angle_other_deg 0.786 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 329 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing