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Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 288 Crystallised with PEG8000
Cryoprotectant PEG400
Crystal Properties Matthews coefficient Solvent content 2.86 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.319 α = 90 b = 67.546 β = 110.21 c = 111.169 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 CCD MARMOSAIC 225 mm CCD 2002-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97842 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.89 29.5 98.3 0.053 9 2.1 67751 22.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 0.329 1.7
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 1.89 29.5 1.35 67722 3424 98.12 0.1746 0.1728 0.172 0.2087 0.2071 29.89
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 20.8108 f_angle_d 1.1551 f_chiral_restr 0.0528 f_plane_restr 0.0098 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3385 Nucleic Acid Atoms 1840 Solvent Atoms 571 Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling MOLREP phasing