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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH14445
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 MORPHEUS screen condition B9 (0.09 M Halogens, 0.1 M Tris/Bicine pH 8.5, 30 % P500MME_P20K)
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.76 α = 90 b = 80.85 β = 90 c = 170.847 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 2024-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7749 MAX IV BioMAX
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 2.64 85.424 100 0.998 10.7 11.4 33478
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 2.64 2.69 0.333
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 (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 2.64 42.75 31626 1760 99.72 0.24832 0.24582 0.2481 0.29361 0.2939 RANDOM 83.091
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] 2.42 -1.55 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.45 r_dihedral_angle_2_deg 11.174 r_long_range_B_other 7.369 r_long_range_B_refined 7.368 r_dihedral_angle_1_deg 6.5 r_mcangle_it 4.606 r_mcangle_other 4.606 r_scangle_other 3.757 r_mcbond_it 2.649 r_mcbond_other 2.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.45 r_dihedral_angle_2_deg 11.174 r_long_range_B_other 7.369 r_long_range_B_refined 7.368 r_dihedral_angle_1_deg 6.5 r_mcangle_it 4.606 r_mcangle_other 4.606 r_scangle_other 3.757 r_mcbond_it 2.649 r_mcbond_other 2.649 r_scbond_it 2.091 r_scbond_other 2.087 r_angle_refined_deg 1.007 r_angle_other_deg 0.377 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7386 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing