Experiment: 9WEM

Plasmodium vivax aspartyl-tRNA synthetase in combination with Asp-AMS, Mg ion, MOPS and PGE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Morepheus F5: 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) and 0.12 M Monosaccharides (0.2 M D-Glucose; 0.2 M D-Mannose; 0.2 M D-Galactose; 0.2 M L-Fucose; 0.2 M D- Xylose; 0.2 M N-Acetyl-D-Glucosamine)

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.008	α = 90
b = 139.008	β = 90
c = 273.343	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		2023-03-17	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)	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	2.128	120.384	100	0.997	10.5	40.6		87793

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	2.128	2.165	100		0.376	0.5	41.9

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	2.128	55.086	1.33	87241	4382	99.38	0.1984	0.1971	0.2018	0.2244	0.2289

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	5.156
f_angle_d	0.61
f_chiral_restr	0.044
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8154
Nucleic Acid Atoms
Solvent Atoms	588
Heterogen Atoms	104

Software

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