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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH011247
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.09M Halogens 0.1M Buffer System 1 pH 6.5 30.0%v/v GOL_P4K (Morpheus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.35 α = 90 b = 81.397 β = 90 c = 168.405 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 PILATUS3 6M 2021-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9688 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 2.5 40.732 100 0.996 10.5 11.3 39517
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 0.637 2
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 6G40 2.5 40.732 39452 1906 99.954 0.254 0.2518 0.2532 0.2946 0.2944 56.748
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] -0.654 1.223 -0.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.463 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 16.78 r_dihedral_angle_1_deg 5.66 r_lrange_it 3.947 r_lrange_other 3.941 r_mcangle_it 2.189 r_mcangle_other 2.189 r_scangle_it 1.452 r_scangle_other 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.463 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 16.78 r_dihedral_angle_1_deg 5.66 r_lrange_it 3.947 r_lrange_other 3.941 r_mcangle_it 2.189 r_mcangle_other 2.189 r_scangle_it 1.452 r_scangle_other 1.452 r_mcbond_it 1.2 r_mcbond_other 1.2 r_angle_refined_deg 1.181 r_angle_other_deg 1.058 r_scbond_it 0.761 r_scbond_other 0.76 r_symmetry_nbd_other 0.167 r_nbd_refined 0.159 r_nbtor_refined 0.152 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.072 r_symmetry_xyhbond_nbd_other 0.066 r_symmetry_nbd_refined 0.063 r_chiral_restr 0.036 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 7148 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing