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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 7.2 293 30-35 % PEG 3350,
0.3-0.5 M NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.38 α = 90 b = 87.46 β = 92.59 c = 52.8 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 293 IMAGE PLATE MAR scanner 345 mm plate 2005-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571
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 3 50 97.7 0.08 13.5 3.1 7417 -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) 3 3.1 79.7 0.324 3.67 2.4
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 PDB ENTRY 2HRA PDB ENTRY 2HQT 3 52.7 -3 7210 7075 342 98.1 0.198 0.195 0.2084 0.251 0.2449 RANDOM 39.01
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] -1.25 -0.22 -0.15 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 21.193 r_dihedral_angle_3_deg 20.472 r_dihedral_angle_1_deg 6.873 r_angle_refined_deg 1.317 r_scangle_it 1.151 r_angle_other_deg 0.926 r_mcangle_it 0.767 r_scbond_it 0.721 r_mcbond_it 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 21.193 r_dihedral_angle_3_deg 20.472 r_dihedral_angle_1_deg 6.873 r_angle_refined_deg 1.317 r_scangle_it 1.151 r_angle_other_deg 0.926 r_mcangle_it 0.767 r_scbond_it 0.721 r_mcbond_it 0.43 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_other 0.191 r_nbd_other 0.184 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.129 r_nbtor_other 0.09 r_chiral_restr 0.066 r_mcbond_other 0.049 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 2306 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing