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tRNA-Guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-4-(2-((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)ethyl)-2-(methylamino)-1H-imidazo[4,5-g]quinazolin-8(7H)-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 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.657 α = 90 b = 64.82 β = 93.964 c = 71.808 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 2018-12-07 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 1.54 42.63 97.6 0.998 13.07 3.1 55577 22.09
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 1.54 1.64 0.864
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 1.54 42.63 1.37 55567 2777 97.57 0.1508 0.1491 0.1522 0.1834 0.1862 28.7
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 19.2372 f_angle_d 1.0017 f_chiral_restr 0.0529 f_bond_d 0.0081 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2685 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing