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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 2HRA PDB entry 2HRA PDB entry 2HQT experimental model PDB 2HQT PDB entry 2HRA PDB entry 2HQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 30-35 % PEG 3350, 0.3-0.5 M NaSCN, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.32 α = 90 b = 86.31 β = 99.37 c = 47.12 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 100 IMAGE PLATE MAR scanner 345 mm plate Osmic VariMax Multilayer 2006-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179
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 2.05 45 99.9 0.038 27.45 4.1 20000 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.1 100 0.28 5.75 4 1396
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 (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 2HRA
PDB entry 2HQT 2.05 45 -3 18999 18982 1019 99.91 0.19386 0.19386 0.19065 0.2 0.25552 0.2612 RANDOM 26.461
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] -1.16 0.31 -0.57 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 21.71 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 5.118 r_scangle_it 1.898 r_scbond_it 1.228 r_angle_refined_deg 1.023 r_mcangle_it 0.978 r_angle_other_deg 0.855 r_mcbond_it 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 21.71 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 5.118 r_scangle_it 1.898 r_scbond_it 1.228 r_angle_refined_deg 1.023 r_mcangle_it 0.978 r_angle_other_deg 0.855 r_mcbond_it 0.585 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.183 r_nbd_other 0.18 r_symmetry_vdw_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_other 0.111 r_mcbond_other 0.086 r_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2314 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing