Experiment: 7V8K

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with L-Proline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XIF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine monohydrochloride, 0.2M DL-Serine), 0.1 M Buffer (Imidazole, MES monohydrate), 30 % v/v Precipitant (40% v/v Ethylene glycol, 20% w/v PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.196	α = 90
b = 81.673	β = 102.94
c = 104.66	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 XE 16M		2019-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9197	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	2.47	102	99.9	0.204	1	8.2	6.6		45661

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.47	2.51	100		1.429	0.4	2.3	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5XIF	2.47	68.291	1.35	45591	2267	99.72	0.1693	0.1666	0.2193	0.2361	42.8797

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7661
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	88

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
Auto-Rickshaw	phasing