6LEU

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with 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
2.6152.83

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
1SYNCHROTRONENRAF-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
12.591090.80.07114.53.9940994
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)
12.652.740.479

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 REPLACEMENTNONE4DP32.591040185205388.3690.1930.18890.260939.937
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]
1.514-1.8180.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.278
r_dihedral_angle_4_deg18.488
r_dihedral_angle_3_deg18.19
r_dihedral_angle_1_deg9.078
r_lrange_other8.958
r_lrange_it8.957
r_mcangle_it6.404
r_mcangle_other6.404
r_scangle_it5.598
r_scangle_other5.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.278
r_dihedral_angle_4_deg18.488
r_dihedral_angle_3_deg18.19
r_dihedral_angle_1_deg9.078
r_lrange_other8.958
r_lrange_it8.957
r_mcangle_it6.404
r_mcangle_other6.404
r_scangle_it5.598
r_scangle_other5.598
r_mcbond_it3.972
r_mcbond_other3.965
r_scbond_it3.544
r_scbond_other3.544
r_angle_refined_deg1.79
r_angle_other_deg1.259
r_chiral_restr_other0.753
r_nbd_other0.24
r_symmetry_nbd_refined0.222
r_nbd_refined0.215
r_symmetry_nbd_other0.189
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.162
r_symmetry_xyhbond_nbd_refined0.153
r_chiral_restr0.116
r_symmetry_nbtor_other0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_symmetry_xyhbond_nbd_other0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8875
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms194

Software

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