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Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675
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 0.09 M Halogens, 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 = 80.817 α = 90 b = 81.357 β = 90 c = 169.157 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 6M 2018-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.51 84.58 99.6 0.116 0.126 0.047 0.976 9.3 7 38585
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 2.51 2.56 89.6 0.852 0.918 0.338 0.137 1.8 7.1
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 2.51 84.58 36660 1862 99.49 0.23635 0.23416 0.2359 0.28215 0.2811 RANDOM 73.336
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] 0.67 0.25 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.074 r_dihedral_angle_4_deg 16.145 r_dihedral_angle_3_deg 13.496 r_long_range_B_refined 6.859 r_long_range_B_other 6.859 r_dihedral_angle_1_deg 5.713 r_mcangle_it 4.58 r_mcangle_other 4.58 r_scangle_other 3.578 r_mcbond_it 2.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.074 r_dihedral_angle_4_deg 16.145 r_dihedral_angle_3_deg 13.496 r_long_range_B_refined 6.859 r_long_range_B_other 6.859 r_dihedral_angle_1_deg 5.713 r_mcangle_it 4.58 r_mcangle_other 4.58 r_scangle_other 3.578 r_mcbond_it 2.634 r_mcbond_other 2.633 r_scbond_it 2.032 r_scbond_other 2.031 r_angle_refined_deg 1.158 r_angle_other_deg 0.893 r_chiral_restr 0.058 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 122 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing