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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH2829
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PZ1 7PZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 10 % w/v PEG4000, 20 % glycerol, 0.02 M monosaccharide, 0.1 M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.733 α = 90 b = 82.095 β = 90 c = 169.487 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 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 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 2.6 72.993 100 0.998 11.4 13.4 35462
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 0.589
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 7PZ1 2.6 72.993 35384 1773 99.918 0.257 0.2549 0.2564 0.3069 0.3056 75.414
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] -0.401 2.914 -2.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.653 r_dihedral_angle_6_deg 11.195 r_lrange_it 5.672 r_lrange_other 5.665 r_dihedral_angle_1_deg 5.375 r_mcangle_it 3.474 r_mcangle_other 3.473 r_scangle_it 2.666 r_scangle_other 2.666 r_dihedral_angle_2_deg 2.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.653 r_dihedral_angle_6_deg 11.195 r_lrange_it 5.672 r_lrange_other 5.665 r_dihedral_angle_1_deg 5.375 r_mcangle_it 3.474 r_mcangle_other 3.473 r_scangle_it 2.666 r_scangle_other 2.666 r_dihedral_angle_2_deg 2.543 r_mcbond_it 1.983 r_mcbond_other 1.981 r_scbond_it 1.512 r_scbond_other 1.512 r_angle_refined_deg 0.653 r_angle_other_deg 0.233 r_nbtor_refined 0.171 r_nbd_refined 0.17 r_symmetry_nbd_other 0.168 r_nbd_other 0.136 r_xyhbond_nbd_refined 0.117 r_symmetry_nbd_refined 0.103 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_refined 0.054 r_chiral_restr 0.032 r_chiral_restr_other 0.01 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 6953 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing