3FOW

Plasmodium Purine Nucleoside Phosphorylase V66I-V73I-Y160F Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NW4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5292.150.2 M Magnesium chloride, 0.1 M HEPES sodium pH 7.5, 30% v/v 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K
Crystal Properties
Matthews coefficientSolvent content
4.4372.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 234.969α = 90
b = 234.969β = 90
c = 234.969γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152008-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.8500.11713.32743059.4
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)
12.82.90.573.37.7

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 REPLACEMENTTHROUGHOUT1NW42.835.4225982137699.90.1670.1650.202RANDOM43.88
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.292
r_dihedral_angle_3_deg17.611
r_dihedral_angle_4_deg16.996
r_scangle_it7.926
r_dihedral_angle_1_deg6.257
r_scbond_it5.543
r_mcangle_it4.716
r_mcbond_it2.948
r_angle_refined_deg1.5
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.292
r_dihedral_angle_3_deg17.611
r_dihedral_angle_4_deg16.996
r_scangle_it7.926
r_dihedral_angle_1_deg6.257
r_scbond_it5.543
r_mcangle_it4.716
r_mcbond_it2.948
r_angle_refined_deg1.5
r_nbtor_refined0.318
r_nbd_refined0.194
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.097
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3559
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms58

Software

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