4DPH

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with P65 and NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J3KPDB ENTRY 1J3K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.5297PEG4000, NH4OAc, pH 4.5, Microbatch, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.5952.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.951α = 90
b = 156.447β = 90
c = 164.653γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2004-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODECu FINE FOCUS1.54

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
12.3856.7195.80.0556.91.73605511149.8
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)
12.382.4783.30.2921.719685

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1J3K2.3854.6660475307299.080.22220.21890.2864RANDOM48.8601
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]
2.54-1.18-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.074
r_dihedral_angle_3_deg17.739
r_dihedral_angle_4_deg15.623
r_dihedral_angle_1_deg6.747
r_scangle_it3.001
r_scbond_it1.835
r_mcangle_it1.601
r_angle_refined_deg1.489
r_mcbond_it0.863
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.074
r_dihedral_angle_3_deg17.739
r_dihedral_angle_4_deg15.623
r_dihedral_angle_1_deg6.747
r_scangle_it3.001
r_scbond_it1.835
r_mcangle_it1.601
r_angle_refined_deg1.489
r_mcbond_it0.863
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8867
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms168

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing