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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012035
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 Alcohols, 0.1M Buffer System 1 pH 6.5, 30.0 % v/v GOL_P4K
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.459 α = 90 b = 81.533 β = 90 c = 170.145 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 2020-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.5 170.2 100 0.997 8.8 12.6 40059
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 2.6 0.586
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 2.5 85.07 37989 1960 99.86 0.23946 0.23667 0.2408 0.29377 0.2953 RANDOM 69.249
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] 0.96 -1.63 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 15.818 r_long_range_B_refined 8.407 r_long_range_B_other 8.406 r_dihedral_angle_1_deg 6.277 r_mcangle_it 5.878 r_mcangle_other 5.878 r_scangle_other 5.248 r_mcbond_other 3.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 15.818 r_long_range_B_refined 8.407 r_long_range_B_other 8.406 r_dihedral_angle_1_deg 6.277 r_mcangle_it 5.878 r_mcangle_other 5.878 r_scangle_other 5.248 r_mcbond_other 3.653 r_mcbond_it 3.652 r_scbond_it 3.171 r_scbond_other 3.17 r_angle_refined_deg 1.242 r_angle_other_deg 0.925 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 7067 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing