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Adenine glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with an AP site generated by the enzyme acting on purine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U7T 6U7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 PEG 4000, calcium acetate, ethylene glycol, Tris-HCl, beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.38 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.74 α = 90 b = 85.92 β = 90 c = 140.69 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 2021-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.68 43 99.6 0.09 0.998 9.41 6.76 100381 30.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 98.5 1.9 0.313 1.08 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6U7T 1.68 42.96 1.34 100379 2520 99.62 0.2229 0.2224 0.2224 0.2447 0.2448 49.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.5234 f_angle_d 1.0289 f_chiral_restr 0.0516 f_plane_restr 0.0094 f_bond_d 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2673 Nucleic Acid Atoms 423 Solvent Atoms 214 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing