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tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-4-(2-((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)ethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 100 mM MES pH 5.5, 0.5 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.579 α = 90 b = 65.369 β = 96.129 c = 70.564 γ = 90
Symmetry Space Group C 1 2 1
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 2019-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 1.25 22.52 99.4 0.999 15.82 3.7 112100 15.12
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 1.25 1.33 0.807
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 1PUD 1.25 22.52 1.36 112074 5604 99.37 0.122 0.1208 0.1223 0.1438 0.1446 20.09
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 24.2937 f_angle_d 0.9969 f_chiral_restr 0.0714 f_bond_d 0.0069 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2855 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 42
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XDS data scaling PHASER phasing