7FGW

Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with pyrimethamine, NADPH and dUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EIL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52970.2 M Lithium nitrate, 14% (w/v) PEG4000, 0.1 M Bis-Tris propane pH 7.5 and 1% (w/v) benzamidine hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.7755.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.282α = 85.45
b = 101.121β = 83.7
c = 107.208γ = 84.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.153096.30.03125.32.215290225.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2388.30.2432

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 REPLACEMENTFREE R-VALUE4EIL2.1529.291.96139171694287.160.16240.160.208731.82
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.8089
f_angle_d0.998
f_chiral_restr0.0574
f_plane_restr0.0096
f_bond_d0.0086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17839
Nucleic Acid Atoms
Solvent Atoms1531
Heterogen Atoms358

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing