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Crystal structure of human thymine DNA glycosylase TDG in complex with a covalent inhibitor (1S, 5R)-C-2711
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WYW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG3350, 0.1M TRIS, PH 8.5, 0.2M MAGNESIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.697 α = 90 b = 73.96 β = 90 c = 109.472 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 2024-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.14 61.28 98.7 0.097 0.102 0.032 0.999 17.6 10.4 19522
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.26 90.8 1.086 1.156 0.388 0.626 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wyw 2.14 27.95 1.34 19452 1011 98.6 0.2077 0.2057 0.2083 0.2426 0.2457
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.92 f_angle_d 1.093 f_chiral_restr 0.059 f_plane_restr 0.017 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing