5XIK

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with tetrahydro quinazolinone febrifugine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TWA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each divalent cation and 0.1M MOPS/HEPES-Na

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.644	α = 89.46
b = 90.14	β = 80.34
c = 93.201	γ = 76.07

Symmetry
Space Group	P 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	CCD	MARMOSAIC 225 mm CCD		2015-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.96725	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	50	98.7	0.078	0.093	0.051	7.6	3.3		80691

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	97.9		0.5	0.604	0.334	0.764		3.2	3958

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4TWA	2.5	43.76	75422	3988	96.62	0.1876	0.1846	0.244	RANDOM	37.618

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]
-0.77	0.15	-0.1	0.04	-0.15	0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.18
r_dihedral_angle_3_deg	16.857
r_dihedral_angle_4_deg	16.771
r_dihedral_angle_1_deg	7.101
r_angle_refined_deg	1.717
r_angle_other_deg	0.844
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.18
r_dihedral_angle_3_deg	16.857
r_dihedral_angle_4_deg	16.771
r_dihedral_angle_1_deg	7.101
r_angle_refined_deg	1.717
r_angle_other_deg	0.844
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15280
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	224

Software

Software
Software Name	Purpose
MxCuBE	data collection
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data reduction
HKL	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.