2BSX

Crystal structure of the Plasmodium falciparum purine nucleoside phosphorylase complexed with inosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LX7PDB ENTRY 1LX7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510 % PEG 8000, 0.1 M HEPES PH 7.5, 30 % HEXANETRIOL
Crystal Properties
Matthews coefficientSolvent content
2.345.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.117α = 90
b = 95.117β = 90
c = 47.075γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
1220870.08102.527984
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)
122.07800.3552.4

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 1LX7218.91464878891.60.2680.2640.342RANDOM38.57
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]
0.960.480.96-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.3
r_dihedral_angle_3_deg19.971
r_dihedral_angle_4_deg17.495
r_dihedral_angle_1_deg8.281
r_scangle_it3.808
r_scbond_it3.004
r_angle_refined_deg1.931
r_mcangle_it1.678
r_mcbond_it1.002
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.3
r_dihedral_angle_3_deg19.971
r_dihedral_angle_4_deg17.495
r_dihedral_angle_1_deg8.281
r_scangle_it3.808
r_scbond_it3.004
r_angle_refined_deg1.931
r_mcangle_it1.678
r_mcbond_it1.002
r_nbtor_refined0.321
r_nbd_refined0.292
r_symmetry_vdw_refined0.282
r_xyhbond_nbd_refined0.271
r_symmetry_hbond_refined0.238
r_chiral_restr0.11
r_bond_refined_d0.018
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1847
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing