3U40

Crystal structure of a purine nucleoside phosphorylase from Entamoeba histolytica bound to adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TL6PDB ENTRY 3TL6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289EnhiA.01033.a.MB1 PW30572 at 22 mg/mL with 10 mM adenosine against PACT screen condition E5: 0.2 M sodium nitrate, 20% PEG3350, cryoprotectant: 25% ethylene glycol, crystal tracking ID 225630e5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2946.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.277α = 90
b = 101.202β = 90
c = 167.264γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252011-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
12.055097.90.104166.690147
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)
12.052.1284.40.512.33.67631

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 3TL62.055090061452197.690.18180.17980.2186RANDOM24.9354
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]
-1.361.4-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.407
r_dihedral_angle_3_deg15.444
r_dihedral_angle_4_deg13.854
r_dihedral_angle_1_deg6.118
r_angle_refined_deg1.522
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10461
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms147

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling