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Crystal structure of the editing domain of threonyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QF6 PDB entry 1QF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281 PEG 4000, Tris.cl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.566 α = 90 b = 45.243 β = 90 c = 116.602 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 100 CCD ADSC QUANTUM 4 2003-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9763 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 1.5 40.8 85.8 0.077 4 32601 32601 14.4
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) 1.5 1.55 79 0.382 2933
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1QF6 1.5 40.8 32539 32539 2272 86 0.203 0.203 0.202 0.2037 0.224 0.2263 RANDOM 17.3
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] -1.1 3.15 -2.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.92 c_scbond_it 1.95 c_mcangle_it 1.79 c_angle_deg 1.3 c_mcbond_it 1.19 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.92 c_scbond_it 1.95 c_mcangle_it 1.79 c_angle_deg 1.3 c_mcbond_it 1.19 c_improper_angle_d 0.83 c_bond_d 0.006 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 1805 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing