Experiment: 9WEH

Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, SO4, MOPSO and Butanetriol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Morpheus II-A1: Butanetriol 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) and 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate)

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.779	α = 90
b = 139.779	β = 90
c = 274.11	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.094	121.052	100	0.294	0.999	13.3	40.8		93328

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.094	2.13	100		0.315	0.5	42.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.094	50.459	1.33	92673	4583	99.31	0.1769	0.1751	0.1823	0.2106	0.2118

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.362
f_angle_d	0.739
f_chiral_restr	0.047
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8078
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	160

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
autoPROC	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction