1ODL

PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.3291MICROBATCH METHOD UNDER OIL WAS USED.15.1 MG/ML OF PROTEIN SOLUTION CONTAINING 0.02M DTT WAS MIXED WITH 1.65M SODIUM ACETATE AND 0.1M MES PH 6.3. THE CRYSTALLIZATION TEMPERATURE WAS 291 K. PARATONE-N OIL MIXED WITH 10% W/W OF GLYCEROL WAS USED FOR CRYOPROTECTION SULFATE ION BOUND CRYSTALS WERE OBTAINED BY 7 H SOAKING OF NATIVE CRYSTALS IN SOLUTION CONTAINING 1.2M SODIUM ACETATE PH 6.3 AND 20MM AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
2.549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.002α = 90
b = 132.002β = 90
c = 170.145γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE, RAXIS-VIIMIRRORS2003-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D

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
12.13098.70.115.26.59869454
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)
12.12.1897.70.3315.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.119.9986779438498.80.1870.1870.234RANDOM21.9
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]
0.240.24-0.48
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it5.07
c_scbond_it3.72
c_mcangle_it3.09
c_mcbond_it2.23
c_angle_deg1.3
c_improper_angle_d0.83
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it5.07
c_scbond_it3.72
c_mcangle_it3.09
c_mcbond_it2.23
c_angle_deg1.3
c_improper_angle_d0.83
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10716
Nucleic Acid Atoms
Solvent Atoms713
Heterogen Atoms82

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing