5T0L

Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF and 5-(4-(3,4-dichlorophenyl)piperazin-1-yl)pyrimidine-2,4-diamine (TRC-15)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.3293PEG3350, sodium citrate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.3848.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.277α = 90
b = 143.983β = 90
c = 170.214γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

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
13.125092.40.12711.44.321429
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)
13.123.230.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4EIL3.13109.9320296110192.280.253720.252570.27423RANDOM75.628
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]
1.79-6.64.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.859
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg16.28
r_long_range_B_refined7.891
r_dihedral_angle_1_deg5.319
r_mcangle_it3.46
r_scbond_it2.059
r_mcbond_it1.986
r_angle_refined_deg1.081
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.859
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg16.28
r_long_range_B_refined7.891
r_dihedral_angle_1_deg5.319
r_mcangle_it3.46
r_scbond_it2.059
r_mcbond_it1.986
r_angle_refined_deg1.081
r_chiral_restr0.066
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8142
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing