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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH12163
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 Alcohols, 0.1 M imidazole/MES pH 6.5, 50 % EDO_P8K
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.39 α = 90 b = 81.48 β = 90 c = 170.19 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 2020-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 1.0332 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 2.25 73.4 100 0.999 15.2 13.4 54738
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 2.25 2.29 0.736
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 73.4 54737 2588 99.993 0.202 0.1998 0.2522 0.2491 57.427
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] 0.33 0.008 -0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.621 r_dihedral_angle_6_deg 15.591 r_lrange_other 12.063 r_lrange_it 12.06 r_dihedral_angle_2_deg 11.177 r_scangle_it 9.216 r_scangle_other 9.215 r_mcangle_it 8.497 r_mcangle_other 8.496 r_dihedral_angle_1_deg 8.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.621 r_dihedral_angle_6_deg 15.591 r_lrange_other 12.063 r_lrange_it 12.06 r_dihedral_angle_2_deg 11.177 r_scangle_it 9.216 r_scangle_other 9.215 r_mcangle_it 8.497 r_mcangle_other 8.496 r_dihedral_angle_1_deg 8.009 r_scbond_it 6.265 r_scbond_other 6.264 r_mcbond_it 5.963 r_mcbond_other 5.956 r_angle_refined_deg 1.552 r_angle_other_deg 0.524 r_nbd_refined 0.227 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.186 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.172 r_symmetry_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7522 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing