3EMV

Crystal structure of Plasmodium vivax PNP with sulphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B94PDB ENTRY 2B94

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529118% PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
1.8533.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.749α = 90
b = 94.749β = 90
c = 121.254γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.0745SRSPX10.1

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
11.8567.8880.50.0950.09517.661461914619226.2
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)
1.851.92490.2340.2344.34.4

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 2B941.8533.98146191386075980.380.1930.194710.192690.23277RANDOM24.307
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]
-2.66-1.33-2.663.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_1_deg20.043
r_dihedral_angle_3_deg15.7
r_dihedral_angle_4_deg13.905
r_scangle_it2.797
r_scbond_it1.896
r_angle_refined_deg1.611
r_mcangle_it1.108
r_mcbond_it0.712
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_1_deg20.043
r_dihedral_angle_3_deg15.7
r_dihedral_angle_4_deg13.905
r_scangle_it2.797
r_scbond_it1.896
r_angle_refined_deg1.611
r_mcangle_it1.108
r_mcbond_it0.712
r_nbtor_refined0.301
r_symmetry_vdw_refined0.215
r_nbd_refined0.195
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.148
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms1921
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms5

Software

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