Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Mg ion, Ethylene glycols and Unit cell contraction due to data collected outside the cryo loop


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293Morpheus E12: 0.1 M Buffer System 3 pH 8.5 (Tris and BICINE) 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.12 M Ethylene glycols (0.3 M Diethylene glycol; 0.3 M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3 M Pentaethylene glycol)
Crystal Properties
Matthews coefficientSolvent content
2.9658.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.482α = 90
b = 136.482β = 90
c = 273.354γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.201118.1971000.99914.540.576665
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2012.2391000.3850.741.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.20189.4031.3376143384899.320.18010.17830.18970.21450.2179
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_d4.852
f_angle_d0.872
f_chiral_restr0.051
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8037
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms141

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PDB_EXTRACTdata extraction