6NRZ

Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A74 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5287ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM adenosine, then was mixed 1:1 with MorpheusB6opt1(e12): 11.1% (w/v) PEG 8000, 22.2% (v/v) ethylene glycol, 0.03 M each sodium fluoride, sodium bromide, sodium iodide, 0.1 M MOPE/HEPES-Na, pH=7.5. Tray: 300518e12, puck: ytb8-4. Crystallization of protein from strain UCH-1/proctitis and strain D/UW-3/Cx gave the same data.
Crystal Properties
Matthews coefficientSolvent content
3.1260.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.17α = 90
b = 57.52β = 96.68
c = 139.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2018-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.149.27599.80.0710.0820.99711.764.2148863244.54
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)RedundancyNumber Unique Reflections (All)
12.12.1599.70.5970.6830.7432.354.236

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3A742.149.2751.3588605199599.820.16080.160.197RANDOM51.3004
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 AtomsNumber
Protein Atoms8063
Nucleic Acid Atoms
Solvent Atoms569
Heterogen Atoms199

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing