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Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 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 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159 α = 90 b = 68.7 β = 102.8 c = 227.2 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 PIXEL DECTRIS PILATUS3 2M 2015-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.1 50 98.6 0.02 0.97 5.2 3.5 43333
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.23 98.5 1 0.39 1.1 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AQ7 3.1 221.55 41189 2144 98.58 0.24293 0.24113 0.27753 0.2495 RANDOM 70.008
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] -0.99 -1.32 3.85 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.193 r_dihedral_angle_3_deg 11.729 r_dihedral_angle_4_deg 10.127 r_dihedral_angle_1_deg 4.919 r_long_range_B_refined 2.847 r_long_range_B_other 2.847 r_mcangle_it 1.777 r_mcangle_other 1.777 r_scangle_other 1.297 r_mcbond_it 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.193 r_dihedral_angle_3_deg 11.729 r_dihedral_angle_4_deg 10.127 r_dihedral_angle_1_deg 4.919 r_long_range_B_refined 2.847 r_long_range_B_other 2.847 r_mcangle_it 1.777 r_mcangle_other 1.777 r_scangle_other 1.297 r_mcbond_it 0.955 r_mcbond_other 0.955 r_angle_refined_deg 0.895 r_angle_other_deg 0.886 r_scbond_it 0.71 r_scbond_other 0.71 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13594 Nucleic Acid Atoms 3350 Solvent Atoms Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing