6KP7

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12154


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH297NaOAc, NH2OAc, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.652.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.885α = 90
b = 156.288β = 90
c = 165.288γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123CCDADSC QUANTUM 3152016-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.975098.80.0550.060.02414.35.9105672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.04910.4350.480.2010.9165.3

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 REPLACEMENTNONE4DP31.9726.11102018511195.4450.1960.19430.232633.555
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]
0.0190.065-0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_4_deg16.439
r_dihedral_angle_3_deg16.004
r_dihedral_angle_1_deg8.24
r_lrange_other7.886
r_lrange_it7.884
r_scangle_it5.69
r_scangle_other5.689
r_mcangle_it4.927
r_mcangle_other4.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_4_deg16.439
r_dihedral_angle_3_deg16.004
r_dihedral_angle_1_deg8.24
r_lrange_other7.886
r_lrange_it7.884
r_scangle_it5.69
r_scangle_other5.689
r_mcangle_it4.927
r_mcangle_other4.926
r_scbond_it3.692
r_scbond_other3.692
r_mcbond_it3.355
r_mcbond_other3.355
r_chiral_restr_other1.948
r_angle_refined_deg1.772
r_angle_other_deg1.389
r_symmetry_nbd_refined0.245
r_nbd_other0.219
r_nbd_refined0.21
r_symmetry_nbd_other0.181
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_refined0.175
r_xyhbond_nbd_refined0.159
r_chiral_restr0.134
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.064
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8767
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
DENZOdata reduction
PHASERphasing