6LHJ

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with C452 (compound 16) and NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DP3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2980.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5651.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.277α = 90
b = 156.483β = 90
c = 164.449γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNonius Kappa CCD2003-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
12.41099.10.99415.75.758202
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)
12.42.470.616

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 REPLACEMENTNONE4DP32.41055641278194.6050.1740.17280.202645.957
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]
2.96-1.008-1.951
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.812
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg17.129
r_lrange_it8.779
r_lrange_other8.779
r_dihedral_angle_1_deg7.797
r_scangle_it5.882
r_scangle_other5.882
r_mcangle_it5.55
r_mcangle_other5.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.812
r_dihedral_angle_4_deg19.477
r_dihedral_angle_3_deg17.129
r_lrange_it8.779
r_lrange_other8.779
r_dihedral_angle_1_deg7.797
r_scangle_it5.882
r_scangle_other5.882
r_mcangle_it5.55
r_mcangle_other5.549
r_scbond_it3.844
r_scbond_other3.843
r_mcbond_it3.655
r_mcbond_other3.655
r_angle_refined_deg1.696
r_chiral_restr_other1.326
r_angle_other_deg1.268
r_symmetry_xyhbond_nbd_refined0.278
r_xyhbond_nbd_refined0.249
r_nbd_other0.244
r_nbd_refined0.21
r_symmetry_nbd_other0.194
r_symmetry_nbd_refined0.194
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_other0.176
r_symmetry_nbtor_other0.079
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9036
Nucleic Acid Atoms
Solvent Atoms708
Heterogen Atoms188

Software

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