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Native Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1
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 8.5 294 0.12 M Ethylene glycols, 0.1 M Buffer System 3 pH 8.5 and 50 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.4 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.769 α = 90 b = 81.213 β = 90 c = 167.531 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 2018-02-23 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 2.06 83.77 99.9 0.089 0.093 0.026 0.999 16.9 12.5 68950
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 2.06 2.09 95.7 0.879 0.93 0.299 0.334 2 9.6
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 2.1 83.77 61280 3139 98.88 0.2237 0.22116 0.2277 0.27378 0.2752 RANDOM 43.615
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] -0.99 -0.75 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.669 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 14.015 r_dihedral_angle_1_deg 5.735 r_long_range_B_refined 5.428 r_long_range_B_other 5.396 r_mcangle_it 3.321 r_mcangle_other 3.32 r_scangle_other 3.267 r_mcbond_it 1.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.669 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 14.015 r_dihedral_angle_1_deg 5.735 r_long_range_B_refined 5.428 r_long_range_B_other 5.396 r_mcangle_it 3.321 r_mcangle_other 3.32 r_scangle_other 3.267 r_mcbond_it 1.985 r_mcbond_other 1.983 r_scbond_it 1.931 r_scbond_other 1.931 r_angle_refined_deg 1.06 r_angle_other_deg 0.739 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 7455 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing