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Mutant T252A 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 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 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.25 α = 90 b = 68.91 β = 104.93 c = 228.33 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 PILATUS 6M 2015-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 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 2.6 220.62 99.8 0.121 0.992 7.8 3.5 73538
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 2.6 2.69 99.9 0.763 0.66 1.5 3.69
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 2.6 220.62 69873 3665 99.8 0.22092 0.21867 0.26416 0.2467 RANDOM 59.569
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] 0.28 0.24 0.37 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_dihedral_angle_3_deg 15.271 r_dihedral_angle_4_deg 14.593 r_dihedral_angle_1_deg 5.673 r_long_range_B_refined 5.177 r_long_range_B_other 5.177 r_mcangle_it 3.622 r_mcangle_other 3.622 r_scangle_other 3.174 r_mcbond_it 2.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_dihedral_angle_3_deg 15.271 r_dihedral_angle_4_deg 14.593 r_dihedral_angle_1_deg 5.673 r_long_range_B_refined 5.177 r_long_range_B_other 5.177 r_mcangle_it 3.622 r_mcangle_other 3.622 r_scangle_other 3.174 r_mcbond_it 2.092 r_mcbond_other 2.092 r_scbond_it 1.868 r_scbond_other 1.868 r_angle_refined_deg 1.131 r_angle_other_deg 0.973 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 13666 Nucleic Acid Atoms 3409 Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing