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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with activator TH10785
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 8.5 293.15 0.06 M Divalents, 0.1 M Buffer System 3 pH 8.5, 30 % v/v Precipitant Mix 2 (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.833 α = 90 b = 81.802 β = 90 c = 170.643 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 S 6M 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9780 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 85.3 100 0.082 0.088 0.034 1 18.3 12.8 35633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 0.986 1.07 0.412 0.87 2.2
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 6G3Y 2.6 73.873 35550 1850 99.944 0.239 0.2368 0.2377 0.2861 0.2876 73.594
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] -2.627 5.572 -2.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.737 r_dihedral_angle_4_deg 15.604 r_dihedral_angle_3_deg 13.03 r_lrange_it 7.888 r_lrange_other 7.888 r_dihedral_angle_1_deg 6.325 r_mcangle_it 5.327 r_mcangle_other 5.326 r_scangle_it 4.504 r_scangle_other 4.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.737 r_dihedral_angle_4_deg 15.604 r_dihedral_angle_3_deg 13.03 r_lrange_it 7.888 r_lrange_other 7.888 r_dihedral_angle_1_deg 6.325 r_mcangle_it 5.327 r_mcangle_other 5.326 r_scangle_it 4.504 r_scangle_other 4.503 r_mcbond_it 3.202 r_mcbond_other 3.2 r_scbond_it 2.656 r_scbond_other 2.656 r_angle_refined_deg 1.227 r_angle_other_deg 1.084 r_nbd_other 0.236 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.178 r_symmetry_nbd_other 0.172 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.155 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7381 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing