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Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with 71g
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.15 M Ammonium sulfate, 0.1 M HEPES pH7.5, 25% w/v PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.176 α = 90 b = 79.272 β = 105.71 c = 77.616 γ = 90
Symmetry Space Group P 1 21 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 6M 2024-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
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 1.82 53.88 99.9 0.062 17.9 6.5 63719
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 1.82 1.92 0.72
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 1.82 53.88 60516 3157 99.91 0.19013 0.18906 0.1926 0.21046 0.2158 RANDOM 29.086
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] -1.54 -1.06 2.79 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.402 r_dihedral_angle_4_deg 19.394 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_1_deg 5.385 r_long_range_B_refined 4.003 r_long_range_B_other 3.928 r_scangle_other 3.393 r_scbond_it 2.59 r_scbond_other 2.451 r_angle_other_deg 2.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.402 r_dihedral_angle_4_deg 19.394 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_1_deg 5.385 r_long_range_B_refined 4.003 r_long_range_B_other 3.928 r_scangle_other 3.393 r_scbond_it 2.59 r_scbond_other 2.451 r_angle_other_deg 2.337 r_mcangle_it 2.321 r_mcangle_other 2.321 r_mcbond_it 1.808 r_mcbond_other 1.805 r_angle_refined_deg 1.76 r_chiral_restr 0.103 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 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 5043 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing