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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11227.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 10% w/v PEG4000, 20% v/v glycerol, 0.03M of each ethylene glycol, 0.1M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.113 α = 90 b = 81.306 β = 90 c = 170.254 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 EIGER2 X 16M 2022-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 2.3 58.866 100 0.139 0.151 0.057 0.998 9.9 13 50891
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 2.221 0.543 13.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6G3Y 2.3 58.866 50806 2664 99.921 0.244 0.242 0.2775 0.2831 68.536
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] -0.516 0.414 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.982 r_dihedral_angle_6_deg 16.482 r_dihedral_angle_3_deg 15.447 r_lrange_it 12.658 r_mcangle_it 9.434 r_scangle_it 9.011 r_mcbond_it 6.734 r_scbond_it 6.55 r_dihedral_angle_1_deg 6.433 r_angle_refined_deg 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.982 r_dihedral_angle_6_deg 16.482 r_dihedral_angle_3_deg 15.447 r_lrange_it 12.658 r_mcangle_it 9.434 r_scangle_it 9.011 r_mcbond_it 6.734 r_scbond_it 6.55 r_dihedral_angle_1_deg 6.433 r_angle_refined_deg 1.407 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.306 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7375 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling DIALS data reduction