☰ Navigation Tabs
Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13677
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 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.643 α = 90 b = 82.369 β = 90 c = 171.967 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 85.9 94.1 1 13.9 13.8 31051
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 2.71 0.705
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 2.503 85.9 31050 1505 77.099 0.228 0.2252 0.2253 0.2771 0.2771 68.911
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] 0.462 -0.534 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.105 r_dihedral_angle_6_deg 15.498 r_lrange_it 13.479 r_lrange_other 13.479 r_mcangle_other 10.045 r_mcangle_it 10.044 r_scangle_it 9.786 r_scangle_other 9.761 r_dihedral_angle_2_deg 9.62 r_dihedral_angle_1_deg 7.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.105 r_dihedral_angle_6_deg 15.498 r_lrange_it 13.479 r_lrange_other 13.479 r_mcangle_other 10.045 r_mcangle_it 10.044 r_scangle_it 9.786 r_scangle_other 9.761 r_dihedral_angle_2_deg 9.62 r_dihedral_angle_1_deg 7.877 r_mcbond_it 6.542 r_mcbond_other 6.541 r_scbond_it 6.236 r_scbond_other 6.202 r_angle_refined_deg 1.266 r_angle_other_deg 0.43 r_nbd_refined 0.224 r_nbd_other 0.224 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.186 r_ncsr_local_group_2 0.12 r_ncsr_local_group_1 0.117 r_ncsr_local_group_3 0.114 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_other 0.055 r_metal_ion_refined 0.018 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7519 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing