8YQ8

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.62970.1 M Sodium acetate, pH 4.6, 0.2 M Ammonium acetate, 12% Polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
2.5952.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.763α = 90
b = 156.41β = 90
c = 165.065γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 1002022-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER TURBO X-RAY SOURCE1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.126.199.320.0820.99813.55.988097
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141000.4870.9152.44.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.126.09687705442299.3520.1970.19450.2404RANDOM33.374
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]
-0.1440.0370.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.47
r_dihedral_angle_3_deg14.045
r_dihedral_angle_2_deg11.763
r_lrange_it8.301
r_lrange_other8.264
r_dihedral_angle_1_deg7.46
r_scangle_it5.847
r_scangle_other5.847
r_mcangle_it4.357
r_mcangle_other4.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.47
r_dihedral_angle_3_deg14.045
r_dihedral_angle_2_deg11.763
r_lrange_it8.301
r_lrange_other8.264
r_dihedral_angle_1_deg7.46
r_scangle_it5.847
r_scangle_other5.847
r_mcangle_it4.357
r_mcangle_other4.357
r_scbond_it3.795
r_scbond_other3.787
r_mcbond_it2.988
r_mcbond_other2.987
r_dihedral_angle_other_2_deg2.735
r_angle_refined_deg1.834
r_angle_other_deg0.613
r_nbd_other0.224
r_symmetry_nbd_refined0.223
r_nbd_refined0.215
r_symmetry_nbd_other0.191
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.156
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_refined0.079
r_symmetry_xyhbond_nbd_other0.075
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8676
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms198

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
Cootmodel building
PHASERphasing
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling