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Crystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EVL THREONYL-TRNA SYNTHETASE CORE (PDB CODE: 1EVL)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 ammonium sulfate, magnesium chloride, cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.6 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.45 α = 90 b = 101.74 β = 114.4 c = 199.34 γ = 90
Symmetry Space Group P 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 ADSC QUANTUM 4 2001-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 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 3.46 30 97.9 0.063 15.7 3.74 88408 88408 82
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) 3.46 3.58 82.8 0.346 4.7 3.8 8790
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 THREONYL-TRNA SYNTHETASE CORE (PDB CODE: 1EVL) 3.5 29.8 2 87032 78341 7774 90 0.251 0.251 0.2556 0.287 0.2885 RANDOM 94.6
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] -16.92 4.34 29.09 -12.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 6.06 c_mcangle_it 5.12 c_scbond_it 3.83 c_mcbond_it 3.07 c_angle_deg 1.5 c_improper_angle_d 1.33 c_bond_d 0.012 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 6.06 c_mcangle_it 5.12 c_scbond_it 3.83 c_mcbond_it 3.07 c_angle_deg 1.5 c_improper_angle_d 1.33 c_bond_d 0.012 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 26224 Nucleic Acid Atoms 6280 Solvent Atoms 170 Heterogen Atoms 248
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling