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Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Cladosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM cladosporin, then was mixed 1:1 MorpheusB6opt1(e11): 10.96% (w/v) PEG 8000, 21.92% (v/v) ethylene glycol, 0.03 M each sodium fluoride, sodium bromide, sodium iodide, 0.1 M MOPE/HEPES-Na, pH=7.5. Tray: 300519e11, puck: ytb8-10. Crystallization of protein from strain UCH-1/proctitis and strain D/UW-3/Cx gave the same data.
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.58 α = 90 b = 57.51 β = 97 c = 139.55 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 CCD RAYONIX MX-300 Beryllium Lenses 2018-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 49.316 99.8 0.064 0.074 0.998 13.15 3.79 77679 46.243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.8 0.577 0.672 0.797 2.35 3.81
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A74 2.2 49.316 1.34 77666 1999 99.81 0.1652 0.1641 0.1679 0.2073 0.2108 RANDOM 53.1738
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8027 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 234
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction