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Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with a mimic tRNA(Met) and isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 2% TacsimateTM pH 6.0, 0.1 M BIS-TRIS pH 6.5, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.662 α = 78.39 b = 81.206 β = 83.65 c = 106.171 γ = 71.78
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.83 75.92 93.9 0.049 0.069 0.049 0.994 10 1.8 36523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 2.99 96 0.239 0.338 0.239 0.926 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.83 75.92 28351 1393 76.41 0.23848 0.23662 0.2389 0.27772 0.279 RANDOM 65.865
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] 2.22 2.27 -3.72 -4.46 2.6 4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.946 r_dihedral_angle_4_deg 21.765 r_dihedral_angle_3_deg 17.933 r_long_range_B_refined 8.216 r_long_range_B_other 8.215 r_mcangle_it 6.354 r_mcangle_other 6.354 r_scangle_other 6.087 r_dihedral_angle_1_deg 5.482 r_mcbond_it 4.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.946 r_dihedral_angle_4_deg 21.765 r_dihedral_angle_3_deg 17.933 r_long_range_B_refined 8.216 r_long_range_B_other 8.215 r_mcangle_it 6.354 r_mcangle_other 6.354 r_scangle_other 6.087 r_dihedral_angle_1_deg 5.482 r_mcbond_it 4.109 r_mcbond_other 4.109 r_scbond_it 4.038 r_scbond_other 4.037 r_angle_other_deg 1.406 r_angle_refined_deg 1.202 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7608 Nucleic Acid Atoms 1365 Solvent Atoms 7 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing