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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13264
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 6G3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10 % w/v PEG4000, 20 % glycerol, 0.03 M ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.589 α = 90 b = 81.874 β = 90 c = 169.954 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 2.35 58.85 100 0.999 12.1 13.4 48282
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 2.35 2.43 0.576
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 2.35 58.85 48192 2387 99.934 0.265 0.2632 0.2655 0.3024 0.3081 68.685
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] -0.411 2.229 -1.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.232 r_dihedral_angle_6_deg 10.833 r_dihedral_angle_1_deg 5.431 r_lrange_it 4.699 r_lrange_other 4.669 r_mcangle_it 2.845 r_mcangle_other 2.844 r_scangle_it 2.193 r_scangle_other 2.193 r_dihedral_angle_2_deg 2.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.232 r_dihedral_angle_6_deg 10.833 r_dihedral_angle_1_deg 5.431 r_lrange_it 4.699 r_lrange_other 4.669 r_mcangle_it 2.845 r_mcangle_other 2.844 r_scangle_it 2.193 r_scangle_other 2.193 r_dihedral_angle_2_deg 2.076 r_mcbond_it 1.586 r_mcbond_other 1.586 r_scbond_it 1.245 r_scbond_other 1.245 r_angle_refined_deg 0.659 r_angle_other_deg 0.238 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.171 r_nbd_refined 0.169 r_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.13 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.074 r_symmetry_nbd_refined 0.074 r_chiral_restr 0.033 r_chiral_restr_other 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7290 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing