7F3Z

Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QGT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH29728.5% PEG4000, 0.8 M CH3COONH4 0.08 M CH3COONa
Crystal Properties
Matthews coefficientSolvent content
2.4755.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.332α = 90
b = 153.739β = 90
c = 164.119γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2003-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU R-AXIS IV1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.651.54970.0830.99410.14.1743724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.690.523

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 REPLACEMENTFREE R-VALUE3QGT2.639.78243660217897.3730.2010.19790.253157.552
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]
0.322-0.7240.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.228
r_dihedral_angle_3_deg19.775
r_dihedral_angle_4_deg18.773
r_lrange_it8.255
r_lrange_other8.242
r_dihedral_angle_1_deg8.213
r_scangle_it5.915
r_scangle_other5.915
r_mcangle_it5.714
r_mcangle_other5.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.228
r_dihedral_angle_3_deg19.775
r_dihedral_angle_4_deg18.773
r_lrange_it8.255
r_lrange_other8.242
r_dihedral_angle_1_deg8.213
r_scangle_it5.915
r_scangle_other5.915
r_mcangle_it5.714
r_mcangle_other5.713
r_dihedral_angle_other_2_deg4.694
r_scbond_it3.869
r_scbond_other3.869
r_mcbond_it3.772
r_mcbond_other3.768
r_angle_refined_deg1.602
r_angle_other_deg1.166
r_symmetry_nbd_refined0.248
r_nbd_other0.24
r_nbd_refined0.21
r_symmetry_nbd_other0.189
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.114
r_symmetry_xyhbond_nbd_other0.096
r_symmetry_nbtor_other0.079
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9110
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing