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Structure of Thermus thermophilus lysyl-tRNA synthetase complexed with wild-type E.coli tRNALys(mnm5s2UUU) and sulphamoyl-analogue of lysyl-adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 24-26% saturated ammonium sulphate.
50 mM Tris-maleate (pH 7.6), 10 mM MgCI2, 1 mM NaN3, 4 mg/ml
LysRSTT, 2.5 mg/ml wt Ecoli tRNALys and 325 microM LysAMS.
Cryoprotectant 30% glycerol.
Crystal Properties Matthews coefficient Solvent content 4.87 74.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.3 α = 90 b = 147.3 β = 90 c = 127.45 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MAR scanner 300 mm plate 1995-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.885 ESRF ID13
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 3.8 20 99.1 0.104 6.02 3.59 15932
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 3.8 3.9 0.366
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.8 19.929 15932 842 98.895 0.213 0.2117 0.2158 0.2366 0.2352 107.589
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] 1.94 0.97 1.94 -6.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.057 r_dihedral_angle_6_deg 9.671 r_lrange_it 7.062 r_lrange_other 7.061 r_dihedral_angle_1_deg 5.525 r_dihedral_angle_2_deg 4.351 r_scangle_it 3.407 r_scangle_other 3.407 r_mcangle_it 3.382 r_mcangle_other 3.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.057 r_dihedral_angle_6_deg 9.671 r_lrange_it 7.062 r_lrange_other 7.061 r_dihedral_angle_1_deg 5.525 r_dihedral_angle_2_deg 4.351 r_scangle_it 3.407 r_scangle_other 3.407 r_mcangle_it 3.382 r_mcangle_other 3.381 r_mcbond_it 1.905 r_mcbond_other 1.905 r_scbond_it 1.867 r_scbond_other 1.867 r_angle_refined_deg 0.745 r_angle_other_deg 0.283 r_dihedral_angle_other_2_deg 0.219 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.173 r_nbd_refined 0.169 r_xyhbond_nbd_refined 0.132 r_nbd_other 0.096 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.065 r_symmetry_xyhbond_nbd_refined 0.037 r_chiral_restr 0.034 r_chiral_restr_other 0.016 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3971 Nucleic Acid Atoms 411 Solvent Atoms Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing