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Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.025 α = 90 b = 86.025 β = 90 c = 427.602 γ = 90
Symmetry Space Group P 41 21 2
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-F 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 86.03 100 0.299 0.311 0.087 0.998 8.1 24.1 110134 22.48
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 2.03 100 2.65 2.79 0.886 0.529 1.2 19
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6RLW 2 84.478 109736 5445 99.799 0.209 0.207 0.2503 0.2279 27.778
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] -0.456 -0.456 0.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.583 r_dihedral_angle_4_deg 16.054 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 6.871 r_lrange_it 6.023 r_lrange_other 5.995 r_scangle_it 4.209 r_scangle_other 4.209 r_mcangle_it 3.12 r_mcangle_other 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.583 r_dihedral_angle_4_deg 16.054 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 6.871 r_lrange_it 6.023 r_lrange_other 5.995 r_scangle_it 4.209 r_scangle_other 4.209 r_mcangle_it 3.12 r_mcangle_other 3.12 r_scbond_it 2.592 r_scbond_other 2.592 r_mcbond_it 1.975 r_mcbond_other 1.975 r_angle_refined_deg 1.413 r_angle_other_deg 1.279 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_refined 0.204 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.182 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.073 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12158 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing