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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH7420
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 Monosaccharides, 0.1 M bicine/Trizma base pH 8.5, 50 % GOL_P4K
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.501 α = 90 b = 81.598 β = 90 c = 170.355 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 XE 16M 2023-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.4 58.956 100 0.999 16.9 13.3 45246
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 2.4 2.48 0.774
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 2.4 58.956 45178 2258 99.982 0.232 0.2293 0.2292 0.2813 0.281 74.466
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] 1.181 -0.132 -1.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 22.398 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_6_deg 16.069 r_lrange_other 15.009 r_lrange_it 15.005 r_mcangle_it 11.969 r_mcangle_other 11.969 r_scangle_it 10.827 r_scangle_other 10.826 r_mcbond_it 8.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 22.398 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_6_deg 16.069 r_lrange_other 15.009 r_lrange_it 15.005 r_mcangle_it 11.969 r_mcangle_other 11.969 r_scangle_it 10.827 r_scangle_other 10.826 r_mcbond_it 8.05 r_mcbond_other 8.049 r_dihedral_angle_1_deg 7.803 r_scbond_it 7.17 r_scbond_other 7.169 r_dihedral_angle_2_deg 6.517 r_angle_refined_deg 1.432 r_angle_other_deg 0.484 r_nbd_other 0.275 r_nbd_refined 0.226 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.2 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 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 7531 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing