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Ternary complex of E. coli leucyl-tRNA synthetase bound to tRNA(leu) and Leucinol in the editing state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ARI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1M Sodium Acetate pH5.0, 0.2M Ammonium Chloride, 20-24% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.694 α = 90 b = 119.545 β = 90 c = 141.639 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 100 PIXEL DECTRIS PILATUS3 6M Vertical CRL / Horizontal CRL 2024-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.782 70.82 96.3 0.093 0.097 0.027 0.997 15.4 13.2 101703 27.8
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 1.782 1.917 66.7 1.548 1.615 0.455 0.643 1.5 12.4
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 1.782 35.41 101684 5083 81.6 0.2049 0.2033 0.1961 0.2347 0.2257 RANDOM 37.97
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] -0.7008 1.6731 -0.9723
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.72 t_omega_torsion 3.57 t_angle_deg 0.85 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6517 Nucleic Acid Atoms 1711 Solvent Atoms 777 Heterogen Atoms 44
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction STARANISO data scaling PHASER phasing