Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS, Mg ion, Iodides and Pentaethylene glycol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Morpheus B5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) and 0.09 M Halogens (0.3 M Sodium fluoride; 0.3 M Sodium bromide; 0.3 M Sodium iodide)
Crystal Properties
Matthews coefficientSolvent content
3.0759.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.685α = 90
b = 138.685β = 90
c = 274.992γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97627DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.228120.1051000.1960.99716.237.676798
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)
12.2282.2671000.2610.520.9

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-VALUE2.22845.8321.3376368385499.460.19110.18950.1960.22080.2249
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_d5.562
f_angle_d0.704
f_chiral_restr0.047
f_bond_d0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8132
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms74

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PDB_EXTRACTdata extraction