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Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate analogue.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 10 microliter hanging
drops containing 25 mM Tris-maleate/NaOH buffer at
pH 7.2,2.5 mM MgC12,20% saturated (V/V) ammonium
sulphate, 1 mM NaN3, 2.6 mg/ml tRNA(ser) and 5.6
mg/ml seryl-tRNA synthetase (stoichiometric ratio of
1.5 tRNA molecules to one enzyme dimer), were equil-
ibrated at room temperature against 32% saturated ammonium sulphate.
Crystal Properties Matthews coefficient Solvent content 3.55 65.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.04 α = 90 b = 125.81 β = 90 c = 117.62 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 138 IMAGE PLATE MAR scanner 300 mm plate 1994-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.9 LURE DW32
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 2.7 20 90.7 0.069 10.5 3.2 45116 27.77
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 2.7 2.82 48.6 0.225
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 2.7 19.99 1.34 45116 2321 90.51 0.1866 0.1842 0.1842 0.2296 0.2297 40.46
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 18.4441 f_angle_d 0.5305 f_chiral_restr 0.0343 f_plane_restr 0.0052 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6541 Nucleic Acid Atoms 1863 Solvent Atoms 214 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling MOLREP phasing