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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14047
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 293 0.09M Halogens, 0.1M MOPS/HEPES-Na pH 7.5, 50% v/v EDO_P8K (Morpheus Screen, Molecular Dimensions).
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.976 α = 90 b = 80.764 β = 90 c = 166.815 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 2024-03-14 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 2.27 83.407 98.1 0.989 14.1 13.3 49693
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 2.27 2.31 0.759
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.271 83.407 49653 2417 97.993 0.211 0.2081 0.2666 0.2588 62.272
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] -0.321 1.191 -0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.291 r_dihedral_angle_6_deg 15.072 r_lrange_it 12.82 r_lrange_other 12.803 r_dihedral_angle_2_deg 11.068 r_scangle_it 10.33 r_scangle_other 10.288 r_mcangle_other 8.891 r_mcangle_it 8.89 r_scbond_it 7.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.291 r_dihedral_angle_6_deg 15.072 r_lrange_it 12.82 r_lrange_other 12.803 r_dihedral_angle_2_deg 11.068 r_scangle_it 10.33 r_scangle_other 10.288 r_mcangle_other 8.891 r_mcangle_it 8.89 r_scbond_it 7.294 r_dihedral_angle_1_deg 7.235 r_scbond_other 7.189 r_mcbond_it 6.31 r_mcbond_other 6.307 r_angle_refined_deg 1.638 r_angle_other_deg 0.567 r_symmetry_nbd_refined 0.335 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_other 0.23 r_nbd_refined 0.227 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.141 r_ncsr_local_group_2 0.136 r_ncsr_local_group_1 0.124 r_ncsr_local_group_3 0.124 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7476 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing