7VC5

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Febrifugine (FF) at 1.61 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7F9S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine monohydrochloride and 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 coefficientSolvent content
2.5351.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.194α = 90
b = 73.092β = 111.57
c = 74.936γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.6160.3899.90.05115.46.774455
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)
11.611.641002.5110.36.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7F9S1.61253.5621.3574242363899.620.16650.1650.195643.699
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 AtomsNumber
Protein Atoms3888
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms100

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing