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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 norvaline 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 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.65 α = 90 b = 70.62 β = 104.52 c = 230.34 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 MARMOSAIC 225 mm CCD 2015-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 99.6 0.01 0.99 6.1 3.3 45457
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 3.21 99.9 1 0.29 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AQ7 3.1 50 43264 2193 99.62 0.22757 0.22578 0.2277 0.26316 0.263 RANDOM 95.831
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] -0.25 -1.33 0.18 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.872 r_dihedral_angle_3_deg 12.19 r_dihedral_angle_4_deg 11.608 r_dihedral_angle_1_deg 4.99 r_long_range_B_refined 4.31 r_long_range_B_other 4.31 r_mcangle_it 2.847 r_mcangle_other 2.847 r_scangle_other 2.079 r_mcbond_it 1.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.872 r_dihedral_angle_3_deg 12.19 r_dihedral_angle_4_deg 11.608 r_dihedral_angle_1_deg 4.99 r_long_range_B_refined 4.31 r_long_range_B_other 4.31 r_mcangle_it 2.847 r_mcangle_other 2.847 r_scangle_other 2.079 r_mcbond_it 1.552 r_mcbond_other 1.552 r_scbond_it 1.145 r_scbond_other 1.145 r_angle_refined_deg 0.907 r_angle_other_deg 0.899 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 13676 Nucleic Acid Atoms 3538 Solvent Atoms Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing