6LH9

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
1MICROBATCH4.62980.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.70854.6

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
12.6443.95190.60.10310.85.0839860
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)
12.642.750.5

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 REPLACEMENTNONE4DP32.64443.95139860198089.7080.2560.25180.331951.836
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]
27.958-5.781-22.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.991
r_dihedral_angle_4_deg18.94
r_dihedral_angle_3_deg18.485
r_lrange_other10.101
r_lrange_it10.1
r_dihedral_angle_1_deg8.28
r_mcangle_it7.379
r_mcangle_other7.379
r_scangle_it7.14
r_scangle_other7.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.991
r_dihedral_angle_4_deg18.94
r_dihedral_angle_3_deg18.485
r_lrange_other10.101
r_lrange_it10.1
r_dihedral_angle_1_deg8.28
r_mcangle_it7.379
r_mcangle_other7.379
r_scangle_it7.14
r_scangle_other7.139
r_mcbond_it4.701
r_mcbond_other4.7
r_scbond_it4.547
r_scbond_other4.547
r_angle_other_deg2.313
r_angle_refined_deg1.797
r_nbd_other0.27
r_symmetry_nbd_refined0.219
r_symmetry_nbd_other0.216
r_nbd_refined0.209
r_xyhbond_nbd_refined0.181
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_other0.115
r_symmetry_xyhbond_nbd_refined0.102
r_chiral_restr0.092
r_symmetry_nbtor_other0.072
r_bond_other_d0.035
r_gen_planes_other0.026
r_gen_planes_refined0.013
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8818
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms150

Software

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