7F3Y

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with methotrexate (MTX), NADPH and dUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QGT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH297PEG3350, litium chloride, sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.555.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.678α = 90
b = 154.403β = 90
c = 164.165γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

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
12.255096.90.99412.56.666860
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)
12.252.330.926

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3QGT2.25227.57764950324793.9320.1850.18220.232942.303
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]
-0.4320.0850.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.633
r_dihedral_angle_3_deg17.411
r_dihedral_angle_4_deg16.434
r_lrange_other9.392
r_lrange_it9.387
r_dihedral_angle_1_deg7.755
r_mcangle_it6.476
r_mcangle_other6.475
r_scangle_it6.45
r_scangle_other6.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.633
r_dihedral_angle_3_deg17.411
r_dihedral_angle_4_deg16.434
r_lrange_other9.392
r_lrange_it9.387
r_dihedral_angle_1_deg7.755
r_mcangle_it6.476
r_mcangle_other6.475
r_scangle_it6.45
r_scangle_other6.449
r_mcbond_it4.103
r_mcbond_other4.103
r_scbond_it4.093
r_scbond_other4.092
r_dihedral_angle_other_2_deg2.489
r_angle_refined_deg1.613
r_angle_other_deg1.267
r_nbd_other0.242
r_symmetry_nbd_refined0.239
r_nbd_refined0.208
r_symmetry_nbd_other0.192
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.171
r_symmetry_nbtor_other0.079
r_chiral_restr0.077
r_symmetry_xyhbond_nbd_other0.021
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9075
Nucleic Acid Atoms
Solvent Atoms546
Heterogen Atoms247

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing