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Crystal structure of product-bound human OGG1(WT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other DNA-free HsOGG1 structure (see related entry) was used for MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 288 50 mM MES, pH 6.0, 16-23% PEG6000, cryoprotectant: 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.84 56.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.543 α = 90 b = 91.543 β = 90 c = 213.389 γ = 120
Symmetry Space Group P 65 2 2
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 S 6M 2023-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 213.39 99.9 0.125 0.998 14 19.1 36687
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 2.05 98.3 0.421
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 74.32 0.01 32265 1619 88.12 0.1882 0.1853 0.1969 0.2424 0.2503
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 22.96 f_angle_d 1.002 f_chiral_restr 0.057 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms 557 Solvent Atoms 124 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing