Plasmodium vivax aspartyl-tRNA synthetase in complex with L-Asp, Lanthanide, MOPSO and Butanetriol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Morpheous II E1: 0.1 M Buffer System 4 (MOPSO, Bis-Tris) pH 6.5, 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 2 mM Lanthanides [0.005M Yttrium(III) chloride hexahydrate, 0.005M Erbium(III) chloride hexahydrate, 0.005M Terbium(III) chloride hexahydrate, 0.005M Ytterbium(III) chloride hexahydrate]
Crystal Properties
Matthews coefficientSolvent content
3.0559.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.737α = 90
b = 138.737β = 90
c = 272.751γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 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
12.402128.599.50.090.99934.140.460827
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4022.44497.30.8830.9354.4

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 DIFFRACTIONSADFREE R-VALUE2.40248.6281.3560801305899.510.17710.17530.18790.210.2162
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_d5.246
f_angle_d0.879
f_chiral_restr0.053
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8061
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms62

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
autoPROCdata reduction
AutoSolphasing
PDB_EXTRACTdata extraction