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Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to a tRNA(Tyr)(GUA) transcript, the sulphamoyl analogue of tyrosyl-adenylate and pyrophosphate.
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, HANGING DROP 288 Don't know
Crystal Properties Matthews coefficient Solvent content 3.51 64.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.629 α = 90 b = 130.629 β = 90 c = 109.086 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 CCD ADSC QUANTUM 4 2001-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 23 97.06 0.063 8 6.2 29086
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 2.77 97.8 0.352
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 23 29086 1449 97.057 0.206 0.2042 0.2479 0.2775 88.246
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] 1.459 0.73 1.459 -4.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.668 r_dihedral_angle_6_deg 13.167 r_lrange_it 10.292 r_lrange_other 10.291 r_scangle_it 7.725 r_scangle_other 7.724 r_mcangle_it 5.774 r_mcangle_other 5.774 r_dihedral_angle_1_deg 5.609 r_dihedral_angle_2_deg 5.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.668 r_dihedral_angle_6_deg 13.167 r_lrange_it 10.292 r_lrange_other 10.291 r_scangle_it 7.725 r_scangle_other 7.724 r_mcangle_it 5.774 r_mcangle_other 5.774 r_dihedral_angle_1_deg 5.609 r_dihedral_angle_2_deg 5.484 r_scbond_it 4.907 r_scbond_other 4.906 r_mcbond_it 3.802 r_mcbond_other 3.796 r_angle_refined_deg 1.072 r_angle_other_deg 0.381 r_dihedral_angle_other_2_deg 0.283 r_nbtor_refined 0.196 r_nbd_refined 0.191 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.153 r_nbd_other 0.132 r_xyhbond_nbd_refined 0.129 r_symmetry_nbd_refined 0.125 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.046 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3393 Nucleic Acid Atoms 1753 Solvent Atoms Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing