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Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WYW PDB ENTRY 1wyw, SUMO removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 8 mg/ml protein and 20% molar excess DNA duplex in 10mM Tris-HCL, 100 mM NaCl, 0.5mM DTT. Reservoir: 20% PEG 3350, 0.2M K/Na tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.54 65.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.133 α = 90 b = 162.133 β = 90 c = 56.142 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 315 2007-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.91837 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.79 50 99.6 0.083 0.083 25.5 10.4 21137 21137 87.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.89 96.8 1 7.9 2031
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 1wyw, SUMO removed 2.79 50 19458 1048 97.49 0.23211 0.22965 0.2247 0.27629 0.2691 RANDOM 110.074
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] -4.52 -2.26 -4.52 6.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.864 r_dihedral_angle_4_deg 24.614 r_dihedral_angle_3_deg 22.542 r_dihedral_angle_1_deg 9.62 r_scangle_it 2.984 r_angle_refined_deg 2.272 r_scbond_it 1.839 r_mcangle_it 1.66 r_mcbond_it 0.978 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.864 r_dihedral_angle_4_deg 24.614 r_dihedral_angle_3_deg 22.542 r_dihedral_angle_1_deg 9.62 r_scangle_it 2.984 r_angle_refined_deg 2.272 r_scbond_it 1.839 r_mcangle_it 1.66 r_mcbond_it 0.978 r_nbtor_refined 0.338 r_nbd_refined 0.29 r_symmetry_vdw_refined 0.289 r_symmetry_hbond_refined 0.246 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.17 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms 929 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling PHASER phasing