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Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HQT CHAIN C FROM PDB ENTRY 2HQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 293 8 - 14 % PEG 20.000,
1 - 3 % dioxane, 100 mM BICINE, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 9.00
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.48 α = 90 b = 94.48 β = 90 c = 88.47 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2006-02-07 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179 2 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93950 ESRF ID14-4
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 2.2 50 99.3 0.056 21.5 11 20772 -3
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) 2.2 2.3 100 0.263 4.96 11.3
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 CHAIN C FROM PDB ENTRY 2HQT 2.2 50 -3 19862 19731 1039 99.3 0.228 0.225 0.2433 0.279 0.2817 RANDOM 44.68
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] -1.43 -1.43 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_3_deg 16.872 r_dihedral_angle_4_deg 9.659 r_dihedral_angle_1_deg 7.151 r_scangle_it 2.114 r_scbond_it 1.424 r_angle_refined_deg 1.267 r_mcangle_it 1.027 r_angle_other_deg 0.933 r_mcbond_it 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_3_deg 16.872 r_dihedral_angle_4_deg 9.659 r_dihedral_angle_1_deg 7.151 r_scangle_it 2.114 r_scbond_it 1.424 r_angle_refined_deg 1.267 r_mcangle_it 1.027 r_angle_other_deg 0.933 r_mcbond_it 0.905 r_symmetry_vdw_other 0.261 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.191 r_nbtor_refined 0.182 r_mcbond_other 0.108 r_nbtor_other 0.091 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2203 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing SOLVE phasing RESOLVE phasing Coot model building