3ENZ

Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NW4PDB entry 1NW4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52914.0M Sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
2.9958.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.82α = 90
b = 177.82β = 90
c = 253.868γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.196SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.03145.8699.40.1060.10618.510.7129248129248233.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.199.80.5560.5562.78

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1NW42.03145.86129248122746650299.370.162010.160350.160350.19325RANDOM16.879
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]
-0.08-0.080.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.925
r_dihedral_angle_4_deg20.515
r_dihedral_angle_3_deg13.305
r_dihedral_angle_1_deg6.698
r_scangle_it3.584
r_scbond_it2.28
r_angle_refined_deg1.396
r_mcangle_it1.235
r_mcbond_it0.72
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.925
r_dihedral_angle_4_deg20.515
r_dihedral_angle_3_deg13.305
r_dihedral_angle_1_deg6.698
r_scangle_it3.584
r_scbond_it2.28
r_angle_refined_deg1.396
r_mcangle_it1.235
r_mcbond_it0.72
r_nbtor_refined0.301
r_symmetry_vdw_refined0.229
r_nbd_refined0.198
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.121
r_metal_ion_refined0.119
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11226
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms221

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling