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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545
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 0.12M Alcohols, 0.1M Buffer System 2 pH 7.5, 30.0% v/v EDO_P8K
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.995 α = 90 b = 81.831 β = 90 c = 168.952 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 73 100 0.999 12.8 13.3 47609
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 0.562
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 2.35 57.632 47513 2300 99.91 0.262 0.2597 0.2609 0.31 0.3077 74.348
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] -2.078 1.807 0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.547 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14.947 r_lrange_it 5.98 r_lrange_other 5.971 r_dihedral_angle_1_deg 5.354 r_mcangle_it 3.352 r_mcangle_other 3.352 r_scangle_it 2.593 r_scangle_other 2.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.547 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14.947 r_lrange_it 5.98 r_lrange_other 5.971 r_dihedral_angle_1_deg 5.354 r_mcangle_it 3.352 r_mcangle_other 3.352 r_scangle_it 2.593 r_scangle_other 2.593 r_mcbond_it 1.923 r_mcbond_other 1.923 r_scbond_it 1.462 r_scbond_other 1.462 r_angle_refined_deg 1.165 r_angle_other_deg 1.06 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.166 r_symmetry_nbd_other 0.155 r_nbd_refined 0.153 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.088 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.034 r_symmetry_xyhbond_nbd_other 0.012 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 7121 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing