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Heterodimeric murine tRNA-guanine transglycosylase in complex with queuine and in the presence of Anderson-Evans type (TEW) and Strandberg type polyoxometalate (POM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H62 6H62, 6FV5 experimental model PDB 6FV5 6H62, 6FV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 100 mM Na/K phosphate pH 6.8, 200 mM Sodium chloride, 14 % (w/v) PEG 1000, 1 mM TEW
Crystal Properties Matthews coefficient Solvent content 2.88 57.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.5 α = 90 b = 199.5 β = 90 c = 90.586 γ = 120
Symmetry Space Group P 62 2 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 PILATUS3 6M 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 2.6 48.6 99.9 1 24.06 12.75 62234 58.92
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 2.6 2.75 0.833
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 6H62, 6FV5 2.6 48.6 1.37 62228 3124 99.86 0.2151 0.2138 0.216 0.2394 0.2407 61.78
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 15.4708 f_angle_d 1.0104 f_chiral_restr 0.0477 f_plane_restr 0.0032 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5555 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 114
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing