5ELO

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and cladosporin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ELN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ HCl, pH = 8.5. Crystals were then soaked in a solution that was the previous crystallizaiton condition suplemented with 3 mM lysine and 2 mM cladopsorin for 24 hours, then cryoprotected with 20% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.5852.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.22α = 90
b = 120.72β = 90.23
c = 143.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2015-08-07MSINGLE 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)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
11.95099.60.09110.984.1194875-320.97
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9599.90.5122.844.2

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5ELN1.947.071.35194872199499.60.2040.2040.24630.01
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.755
f_angle_d1.066
f_chiral_restr0.06
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15928
Nucleic Acid Atoms
Solvent Atoms1969
Heterogen Atoms158

Software

Software
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction