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Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
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 Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.3 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.367 α = 90 b = 86.367 β = 90 c = 432.4 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 EIGER X 16M 2019-02-11 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 86.4 100 0.096 0.1 0.029 1 16.5 21.8 112319
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 99.9 1.22 1.28 0.39 0.846 2.7 20.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1EBM 2 84.837 111929 5560 99.859 0.225 0.2225 0.2296 0.2741 0.2766 41.301
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] -0.888 -0.888 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.938 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 14.025 r_dihedral_angle_1_deg 6.74 r_lrange_it 6.344 r_lrange_other 6.34 r_scangle_it 4.121 r_scangle_other 4.121 r_mcangle_it 3.792 r_mcangle_other 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.938 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 14.025 r_dihedral_angle_1_deg 6.74 r_lrange_it 6.344 r_lrange_other 6.34 r_scangle_it 4.121 r_scangle_other 4.121 r_mcangle_it 3.792 r_mcangle_other 3.79 r_scbond_it 2.595 r_scbond_other 2.584 r_mcbond_it 2.449 r_mcbond_other 2.449 r_angle_refined_deg 1.293 r_angle_other_deg 1.205 r_nbd_refined 0.188 r_symmetry_nbd_other 0.176 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.103 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12267 Nucleic Acid Atoms Solvent Atoms 771 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing