6AQS

Crystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PHCPDB entry 3PHC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6295100 mM tri-sodium citrate, pH 5.6, 200 mM ammonium sulfate, 15% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1943.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.11α = 90
b = 95.11β = 90
c = 135.561γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225HE2017-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5745.191000.9913.711.733133
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)
11.571.61000.751.98

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3PHC1.5745.1931499163399.950.184860.183390.21474RANDOM23.783
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]
-1.42-0.71-1.424.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.64
r_dihedral_angle_4_deg15.152
r_dihedral_angle_3_deg11.604
r_dihedral_angle_1_deg5.917
r_long_range_B_refined4.479
r_long_range_B_other4.478
r_scangle_other2.705
r_mcangle_other2.244
r_mcangle_it2.242
r_scbond_it1.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.64
r_dihedral_angle_4_deg15.152
r_dihedral_angle_3_deg11.604
r_dihedral_angle_1_deg5.917
r_long_range_B_refined4.479
r_long_range_B_other4.478
r_scangle_other2.705
r_mcangle_other2.244
r_mcangle_it2.242
r_scbond_it1.616
r_scbond_other1.615
r_angle_refined_deg1.383
r_mcbond_it1.313
r_mcbond_other1.306
r_angle_other_deg0.914
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1749
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing