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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH7399
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.09 M NPS, 0.1 M imidazole/MES pH 6.5, 50 % MPD_P1K_P3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.371 α = 90 b = 81.769 β = 90 c = 169.985 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 2.5 58.7 100 1 19.8 13.8 40082
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 2.5 2.6 0.597
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 2.5 58.7 40018 2092 99.99 0.24 0.2367 0.2363 0.2967 0.2972 90.722
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] 0.795 0.891 -1.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.736 r_dihedral_angle_6_deg 13.938 r_lrange_it 11.275 r_lrange_other 11.275 r_mcangle_it 8.339 r_mcangle_other 8.338 r_scangle_it 7.161 r_scangle_other 7.145 r_dihedral_angle_other_2_deg 6.721 r_dihedral_angle_1_deg 6.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.736 r_dihedral_angle_6_deg 13.938 r_lrange_it 11.275 r_lrange_other 11.275 r_mcangle_it 8.339 r_mcangle_other 8.338 r_scangle_it 7.161 r_scangle_other 7.145 r_dihedral_angle_other_2_deg 6.721 r_dihedral_angle_1_deg 6.636 r_mcbond_it 5.262 r_mcbond_other 5.261 r_scbond_it 4.437 r_dihedral_angle_2_deg 4.426 r_scbond_other 4.417 r_angle_refined_deg 0.92 r_angle_other_deg 0.326 r_symmetry_xyhbond_nbd_refined 0.267 r_nbd_other 0.214 r_nbd_refined 0.202 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 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 7494 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing