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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013546
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 0.09 M Halogens, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v MPD_P1K_P3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.454 α = 90 b = 80.632 β = 90 c = 165.925 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 2021-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 2.6 82.96 100 0.994 9 11.5 33992
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 2.6 2.72 0.996
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6G3Y 2.6 82.96 32143 1766 99.91 0.26171 0.25934 0.2599 0.30267 0.3045 RANDOM 75.664
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] 2.5 -0.42 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.684 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_4_deg 12.533 r_dihedral_angle_1_deg 5.145 r_long_range_B_refined 3.988 r_long_range_B_other 3.966 r_mcangle_it 2.367 r_mcangle_other 2.366 r_scangle_other 1.736 r_mcbond_it 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.684 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_4_deg 12.533 r_dihedral_angle_1_deg 5.145 r_long_range_B_refined 3.988 r_long_range_B_other 3.966 r_mcangle_it 2.367 r_mcangle_other 2.366 r_scangle_other 1.736 r_mcbond_it 1.32 r_mcbond_other 1.32 r_angle_refined_deg 1.007 r_scbond_it 0.928 r_scbond_other 0.928 r_angle_other_deg 0.863 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 7320 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing