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tRNA-guanine transglycosylase Y106F, C158V mutant in complex with queuine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GEV PDB ENTRY 3GEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 100 mM Tris, 1 mM DTT, 10% DMSO, 12 % PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.662 α = 90 b = 64.486 β = 96.18 c = 71.125 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 113.15 CCD MARMOSAIC 225 mm CCD mirror 2010-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.82 50 94.9 0.045 21.7 3 37328 35405 23.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 78.4 0.363 2.2 2.2 1467
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-free PDB ENTRY 3GEV 1.82 23.824 1 33444 3334 89.41 0.1691 0.1659 0.1674 0.1975 0.1986 Random, 10%
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 12.789 f_angle_d 1.158 f_chiral_restr 0.077 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2726 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 32
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling