6AOI

Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF, and 5-(4-phenylpiperazin-1-yl)-6-propylpyrimidine-2,4-diamine (TRC-2528)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.82930.2 M ammonium citrate, pH 4.6, 15% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4750.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.437α = 90
b = 145.053β = 90
c = 174.503γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979282SSRFBL17U1

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
12.975091.70.1149.82.726892
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)
12.973.080.596

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 REPLACEMENTTHROUGHOUTPDB entry 4EIL2.975025595127189.350.220060.217320.27557RANDOM83.287
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]
-4.99-6.1711.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.463
r_dihedral_angle_3_deg17.921
r_dihedral_angle_4_deg15.763
r_long_range_B_refined9.12
r_dihedral_angle_1_deg6.197
r_mcangle_it4.504
r_scbond_it2.979
r_mcbond_it2.66
r_angle_refined_deg1.135
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.463
r_dihedral_angle_3_deg17.921
r_dihedral_angle_4_deg15.763
r_long_range_B_refined9.12
r_dihedral_angle_1_deg6.197
r_mcangle_it4.504
r_scbond_it2.979
r_mcbond_it2.66
r_angle_refined_deg1.135
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms8172
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms252

Software

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