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Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue in the aminoacylation conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3N PDB ENTRY 1H3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 33 MICROM LEURS, 50 MICROM TRNALEU AND 1 MM LEUCYL-ADENYLATE ANALOGUE MIXED EQUALLY WITH 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 1.9 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.66 α = 90 b = 69.2 β = 104.35 c = 228.84 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2009-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 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 2.5 50 90.3 0.08 11.1 2.9 75711
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) 1 2.5 2.6 76.6 0.52 2.1 2.16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1H3N 2.5 39.69 71885 3826 90.33 0.19075 0.18752 0.1893 0.25031 0.2506 RANDOM 48.175
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] 0.18 -0.07 -0.62 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 19.305 r_dihedral_angle_1_deg 7.282 r_angle_refined_deg 1.77 r_angle_other_deg 1.086 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 19.305 r_dihedral_angle_1_deg 7.282 r_angle_refined_deg 1.77 r_angle_other_deg 1.086 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13670 Nucleic Acid Atoms 3307 Solvent Atoms 169 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing