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Crystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with tRNA(Trp)
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 0.5 M ammonium acetate, 0.1 M HEPES pH 7.5, 16% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.788 α = 98.5 b = 63.206 β = 97.25 c = 91.629 γ = 100.04
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 2024-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97954 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.82 89.51 97.4 0.041 0.05 0.027 0.999 21.2 3.3 30805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.87 0.491 0.61 0.356 0.795 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 8I1Y 2.82 59.12 1.97 30742 1472 97.16 0.238 0.2364 0.2711 0.248 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.485 f_angle_d 1.207 f_chiral_restr 0.069 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4577 Nucleic Acid Atoms 2879 Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data scaling xia2 data reduction MERLOT phasing