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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH9525
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.12 M Monosaccharides, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.45 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.86 α = 90 b = 81.335 β = 90 c = 168.593 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 PILATUS 6M 2018-01-19 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) 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 2.49 81.34 100 0.077 0.083 0.032 0.999 17.2 13 39789
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 2.49 2.55 100 0.948 1.028 0.396 0.525 2.3 12.8
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 (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 1EBM 2.49 81.34 37771 1953 99.94 0.22013 0.21796 0.2201 0.26258 0.2592 RANDOM 82.556
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] 4.12 -0.34 -3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.09 r_dihedral_angle_4_deg 15.842 r_dihedral_angle_3_deg 13.408 r_long_range_B_refined 6.976 r_long_range_B_other 6.976 r_dihedral_angle_1_deg 5.861 r_mcangle_it 4.819 r_mcangle_other 4.819 r_scangle_other 3.979 r_mcbond_other 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.09 r_dihedral_angle_4_deg 15.842 r_dihedral_angle_3_deg 13.408 r_long_range_B_refined 6.976 r_long_range_B_other 6.976 r_dihedral_angle_1_deg 5.861 r_mcangle_it 4.819 r_mcangle_other 4.819 r_scangle_other 3.979 r_mcbond_other 2.84 r_mcbond_it 2.839 r_scbond_it 2.313 r_scbond_other 2.312 r_angle_refined_deg 1.138 r_angle_other_deg 0.89 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7531 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing