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Crystal structure of human OGG1 (WT) in a product bound state in the presence of the agonist F51
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Used DNA-free HsOGG1 structural model (see related entry) for MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 50 mM MES, pH 6.0, 16-23% PEG6000, 100 mM calcium acetate, 4.5 mM F51, cryoprotectant: 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.74 α = 90 b = 90.74 β = 90 c = 210.815 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 PILATUS 6M 2023-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
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 2.1 39.29 100 0.182 0.187 0.042 0.999 13.5 19.7 30916
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 2.1 2.16 100 0.286
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 2.1 39.29 0.01 26708 1342 86.59 0.2088 0.2065 0.2079 0.2507 0.2515
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 20.87 f_angle_d 0.626 f_chiral_restr 0.043 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2498 Nucleic Acid Atoms 557 Solvent Atoms 81 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing