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Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VBM PDB ENTRY 1VBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 3 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6,
100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.05 40.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54 α = 90 b = 62.4 β = 90 c = 194.6 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 110 CCD ADSC QUANTUM 315 2006-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 20 99.5 0.098 0.098 19.1 11.8 34168 -3 39.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 100 0.427 0.427 8.2 12.2
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 (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 1VBM 2.2 19.98 34156 34156 1700 99.6 0.193 0.193 0.1933 0.244 0.2429 RANDOM 40.4
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] 7.6 3.12 -10.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 5.8 c_scbond_it 4.2 c_mcangle_it 3.84 c_mcbond_it 2.83 c_improper_angle_d 1.71 c_angle_deg 1.4 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 5.8 c_scbond_it 4.2 c_mcangle_it 3.84 c_mcbond_it 2.83 c_improper_angle_d 1.71 c_angle_deg 1.4 c_bond_d 0.008 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 5102 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 70
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling AMoRE phasing