7F9R

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95, L-Proline and Febrifugine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XIQ 

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; 0.2M DL-Serine), 0.1 M Buffer (midazole; MES monohydrate) and 30 % v/v Precipitant (40% v/v Ethylene glycol; 20% w/v PEG 8000)
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.83α = 90
b = 73.83β = 111.49
c = 74.7γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8351.3499.71136.851148
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.861000.41.27.1

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 REPLACEMENTTHROUGHOUT5XIQ1.8335.7211.3551142258599.720.16730.16590.192956.1521
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 Atoms3887
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms70

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing