6LHI

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with C466 (compound 42) and NADPH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.62980.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.60652.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.308α = 90
b = 154.488β = 90
c = 163.939γ = 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
12.5946.4190.80.0719.87.87440994
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)
12.592.70.4792.1

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 REPLACEMENTNONE4DP32.5946.4140994208190.1380.2470.24350.311239.668
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]
12.679-14.4491.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_3_deg18.357
r_dihedral_angle_4_deg17.358
r_dihedral_angle_1_deg8.665
r_lrange_it8.657
r_lrange_other8.657
r_mcangle_it6.145
r_mcangle_other6.144
r_scangle_other5.433
r_scangle_it5.432
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_3_deg18.357
r_dihedral_angle_4_deg17.358
r_dihedral_angle_1_deg8.665
r_lrange_it8.657
r_lrange_other8.657
r_mcangle_it6.145
r_mcangle_other6.144
r_scangle_other5.433
r_scangle_it5.432
r_mcbond_it3.822
r_mcbond_other3.82
r_scbond_it3.467
r_scbond_other3.467
r_angle_other_deg2.316
r_angle_refined_deg1.719
r_symmetry_xyhbond_nbd_refined0.489
r_nbd_other0.248
r_symmetry_nbd_other0.226
r_symmetry_nbd_refined0.225
r_nbd_refined0.216
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.158
r_symmetry_nbtor_other0.075
r_chiral_restr0.074
r_symmetry_xyhbond_nbd_other0.046
r_bond_other_d0.034
r_gen_planes_other0.022
r_gen_planes_refined0.011
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8857
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms202

Software

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