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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with TH12161
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 295 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 30% v/v Precipitant Mix 2 (Morpheus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.086 α = 90 b = 81.645 β = 90 c = 169.631 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 2020-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.4 81.64 100 0.999 11.1 26.3 44894
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 2.4 2.49 100 0.64 1.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6G3Y 2.4 73.676 44815 2164 99.973 0.231 0.2296 0.2367 0.2566 0.2642 Random selection 65.957
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] -1.97 -0.705 2.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.647 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 15.436 r_lrange_other 6.963 r_lrange_it 6.962 r_dihedral_angle_1_deg 6.697 r_mcangle_it 4.804 r_mcangle_other 4.804 r_scangle_it 4.364 r_scangle_other 4.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.647 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 15.436 r_lrange_other 6.963 r_lrange_it 6.962 r_dihedral_angle_1_deg 6.697 r_mcangle_it 4.804 r_mcangle_other 4.804 r_scangle_it 4.364 r_scangle_other 4.363 r_mcbond_it 2.983 r_mcbond_other 2.983 r_scbond_it 2.63 r_scbond_other 2.63 r_angle_refined_deg 1.249 r_angle_other_deg 1.136 r_symmetry_xyhbond_nbd_refined 0.253 r_symmetry_nbd_refined 0.246 r_nbd_other 0.207 r_nbd_refined 0.183 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.145 r_ncsr_local_group_2 0.1 r_ncsr_local_group_3 0.1 r_ncsr_local_group_1 0.08 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.052 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7395 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing