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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11233.
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 6.5 294 10% w/v PEG4000, 20% v/v glycerol, 0.03M of each halide, 0.1M MES/imidazole pH 6.5. Morpheus screen, Molecular dimensions.
Crystal Properties Matthews coefficient Solvent content 2.77 55.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.632 α = 90 b = 81.763 β = 90 c = 170.486 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 2022-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 59.077 99.9 0.102 0.11 0.041 0.999 14.1 13.7 83828
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 1.95 1.99 0.372 14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6G3Y 1.95 59.077 83253 4317 99.249 0.246 0.2438 0.2427 0.2825 0.2803 54.783
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] -1.585 2.019 -0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.425 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_2_deg 11.532 r_lrange_it 9.335 r_scangle_it 6.763 r_dihedral_angle_1_deg 6.379 r_mcangle_it 6.171 r_scbond_it 4.57 r_mcbond_it 4.405 r_angle_refined_deg 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.425 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_2_deg 11.532 r_lrange_it 9.335 r_scangle_it 6.763 r_dihedral_angle_1_deg 6.379 r_mcangle_it 6.171 r_scbond_it 4.57 r_mcbond_it 4.405 r_angle_refined_deg 1.348 r_symmetry_xyhbond_nbd_refined 0.393 r_symmetry_nbd_refined 0.321 r_nbtor_refined 0.314 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.069 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7175 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHASER phasing Aimless data scaling DIALS data reduction