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Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other T. thermophilus AspRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 277 ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 3.51 64.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.8 α = 90 b = 222.8 β = 111.8 c = 80.8 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.6 11.5 3.7 2.3 45.7
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 THROUGHOUT T. thermophilus AspRS 2.6 11.5 2 63304 3084 84.1 0.204 0.204 0.2195 0.257 0.2677 RANDOM 46.3
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] 5.06 4.7 -7.6 2.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.6 c_scangle_it 6.3 c_mcangle_it 4.8 c_scbond_it 4.58 c_mcbond_it 3.21 c_angle_deg 1.5 c_improper_angle_d 1.16 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.6 c_scangle_it 6.3 c_mcangle_it 4.8 c_scbond_it 4.58 c_mcbond_it 3.21 c_angle_deg 1.5 c_improper_angle_d 1.16 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9182 Nucleic Acid Atoms 3097 Solvent Atoms 402 Heterogen Atoms 72
Software Software Software Name Purpose ALMN model building TSFGEN model building CNS refinement CCP4 phasing TSFGEN) phasing