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Crystal structure of a bacterial clusterless MutYX bound to an Abasic site analog (THF) opposite d(8-oxo-G)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 100 mM CAPS/Sodium hydroxide [pH 10.5], 1200 mM Sodium phosphate monobasic/800 mM Potassium phosphate dibasic, and 200 mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.832 α = 90 b = 84.137 β = 90 c = 225.742 γ = 90
Symmetry Space Group C 2 2 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 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.55 40 97.6 0.063 0.069 0.026 0.999 12.8 6.9 53001 -3 23.29
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 1.55 1.58 96.7 1.525 1.643 0.607 0.739 1.3 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 37.62 1.91 53001 5122 96.85 0.1773 0.1762 0.1762 0.1971 0.197 35.41
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 22.793 f_angle_d 1.0353 f_chiral_restr 0.0504 f_plane_restr 0.0103 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2141 Nucleic Acid Atoms 438 Solvent Atoms 269 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing