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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH011228
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G3Y 6g3y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.12M Monosaccharides, 0.1M Buffer System 2 (pH 7.5), 30.0% (v/v) GOL_P4K (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.6 52.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.79 α = 90 b = 81.318 β = 90 c = 169.905 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 PILATUS 6M 2019-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.987 Diamond I24
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 2.3 84.9 100 0.99 0.9 24.2 50573
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 2.3 2.38 0.54
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6g3y 2.3 84.95 47864 2577 99.88 0.27747 0.27587 0.30717 0.2932 RANDOM 66.957
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] -0.88 -0.38 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.628 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_4_deg 12.482 r_dihedral_angle_1_deg 4.714 r_long_range_B_refined 3.413 r_long_range_B_other 3.399 r_mcangle_it 1.856 r_mcangle_other 1.856 r_scangle_other 1.169 r_mcbond_it 1.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.628 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_4_deg 12.482 r_dihedral_angle_1_deg 4.714 r_long_range_B_refined 3.413 r_long_range_B_other 3.399 r_mcangle_it 1.856 r_mcangle_other 1.856 r_scangle_other 1.169 r_mcbond_it 1.012 r_mcbond_other 1.012 r_angle_refined_deg 0.945 r_angle_other_deg 0.837 r_scbond_it 0.602 r_scbond_other 0.602 r_chiral_restr 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7166 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing