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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13579
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 294 0.12 M Ethylene Glycols, 0.1 M sodium HEPES/MOPS pH 7.5, 50 % GOL_P4K
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.89 α = 90 b = 81.114 β = 90 c = 170.104 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 EIGER X 16M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 73.2 100 0.997 13.7 13.4 76437
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 2.04 0.727
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 73.158 76300 3760 99.902 0.219 0.2168 0.2241 0.2564 0.264 57.381
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] 1.571 -1.123 -0.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.877 r_dihedral_angle_6_deg 15.172 r_lrange_other 10.955 r_lrange_it 10.95 r_scangle_it 8.246 r_scangle_other 8.246 r_dihedral_angle_2_deg 7.789 r_dihedral_angle_1_deg 7.289 r_mcangle_it 7.222 r_mcangle_other 7.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.877 r_dihedral_angle_6_deg 15.172 r_lrange_other 10.955 r_lrange_it 10.95 r_scangle_it 8.246 r_scangle_other 8.246 r_dihedral_angle_2_deg 7.789 r_dihedral_angle_1_deg 7.289 r_mcangle_it 7.222 r_mcangle_other 7.222 r_scbond_it 5.564 r_scbond_other 5.563 r_mcbond_other 5.293 r_mcbond_it 5.292 r_angle_refined_deg 1.402 r_angle_other_deg 0.469 r_nbd_other 0.237 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.051 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7394 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing