3TL6

Crystal structure of purine nucleoside phosphorylase from Entamoeba histolytica


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OCCPDB ENTRY 3OCC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5289EnhiA.01033.a.MB1 PW30575 at 24.4 mg/mL against JCSG+ screen condition H7: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, with 20% ethylene glycol as cryoprotectant, crystal tracking ID 218267h7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.97α = 90
b = 86.56β = 117.88
c = 102.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

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
12.655098.70.06714.523.94436443802-354.736
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)
12.652.7299.20.5062.9

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 3OCC2.655043801220098.980.21490.21270.2572RANDOM58.8445
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]
6.262.81-4.450.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_3_deg17.046
r_dihedral_angle_4_deg14.738
r_dihedral_angle_1_deg5.752
r_angle_refined_deg1.225
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9889
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms35

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction