☰ Navigation Tabs
Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH8535
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.12M Ethylene Glycols, 0.1M Buffer System 2 pH7.5, 30.0%v/v GOL_P4K (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.191 α = 90 b = 81.827 β = 90 c = 169.555 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 EIGER X 16M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 84.8 100 0.999 15.5 13.4 42365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 0.53
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 6g40 2.45 84.777 42280 2178 99.915 0.255 0.2528 0.2528 0.291 0.2926 83.183
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] -0.841 3.362 -2.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.377 r_dihedral_angle_4_deg 15.167 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_1_deg 5.77 r_lrange_it 5.05 r_lrange_other 5.05 r_mcangle_it 3.204 r_mcangle_other 3.204 r_scangle_it 2.511 r_scangle_other 2.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.377 r_dihedral_angle_4_deg 15.167 r_dihedral_angle_3_deg 14.327 r_dihedral_angle_1_deg 5.77 r_lrange_it 5.05 r_lrange_other 5.05 r_mcangle_it 3.204 r_mcangle_other 3.204 r_scangle_it 2.511 r_scangle_other 2.511 r_mcbond_it 1.839 r_mcbond_other 1.839 r_scbond_it 1.417 r_scbond_other 1.417 r_angle_refined_deg 1.189 r_angle_other_deg 1.064 r_symmetry_nbd_other 0.158 r_nbd_other 0.158 r_nbd_refined 0.152 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.092 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_refined 0.036 r_chiral_restr 0.035 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7090 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing