6LEZ

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 46 and NADPH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.62980.1 mM sodium acetate, pH 4.6, 0.2 M ammonium acetate, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.7755.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.703α = 90
b = 155.878β = 90
c = 164.8γ = 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)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
12.641090.60.10310.85.145387
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)
12.642.690.445

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 REPLACEMENTNONE4DP32.6441039019191587.8130.1920.18760.271450.938
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]
3.883-0.891-2.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.816
r_dihedral_angle_4_deg18.435
r_dihedral_angle_3_deg18.414
r_lrange_other9.778
r_lrange_it9.775
r_dihedral_angle_1_deg8.478
r_mcangle_it7.184
r_mcangle_other7.183
r_scangle_it6.849
r_scangle_other6.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.816
r_dihedral_angle_4_deg18.435
r_dihedral_angle_3_deg18.414
r_lrange_other9.778
r_lrange_it9.775
r_dihedral_angle_1_deg8.478
r_mcangle_it7.184
r_mcangle_other7.183
r_scangle_it6.849
r_scangle_other6.848
r_mcbond_it4.595
r_mcbond_other4.594
r_scbond_it4.391
r_scbond_other4.387
r_angle_refined_deg1.718
r_angle_other_deg1.215
r_chiral_restr_other0.952
r_nbd_other0.269
r_symmetry_nbd_refined0.246
r_nbd_refined0.212
r_symmetry_nbd_other0.187
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.113
r_chiral_restr0.104
r_symmetry_xyhbond_nbd_other0.082
r_symmetry_nbtor_other0.078
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8747
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
Cootmodel building