1ODJ

PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherTHE REFINED STRUCTURE OF PURINE NUCLEOSIDE PEPTIDASE FROM THERMUS THERMOPHILUS WAS USED AS STARTING MODEL FOR REFINEMENT

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 LIGAND BOUND CRYSTALS WERE OBTAINED BY 7 H SOAKING OF NATIVE CRYSTALS IN SOLUTION CONTAINING 1.2M SODIUM ACETATE PH 6.3, 20MM AMMONIUM SULFATE, 2MM MAGNESIUM SULFATE AND 5MM GUANOSINE
Crystal Properties
Matthews coefficientSolvent content
2.549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.757α = 90
b = 132.757β = 90
c = 172.06γ = 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
12.41596.90.11816.94.9958580-0.511.4
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)
12.42.4992.70.3323.9

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 REPLACEMENTTHROUGHOUTTHE REFINED STRUCTURE OF PURINE NUCLEOSIDE PEPTIDASE FROM THERMUS THERMOPHILUS WAS USED AS STARTING MODEL FOR REFINEMENT2.414.9358461296096.80.2210.2210.286RANDOM27.5
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]
-1.85-1.853.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it4.15
c_mcangle_it3.24
c_scbond_it3
c_mcbond_it2.07
c_angle_deg1.4
c_improper_angle_d1.03
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it4.15
c_mcangle_it3.24
c_scbond_it3
c_mcbond_it2.07
c_angle_deg1.4
c_improper_angle_d1.03
c_bond_d0.007
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 Atoms258
Heterogen Atoms150

Software

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