1ODK

PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JE1PDB ENTRY 1JE1

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
Crystal Properties
Matthews coefficientSolvent content
2.549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.919α = 90
b = 131.919β = 90
c = 169.906γ = 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
11.92098.80.058267.2116626-0.59.1
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)
11.91.9797.20.2674

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 1JE11.919.98116505587998.80.180.180.208RANDOM22.5
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]
0.240.24-0.47
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it4.04
c_scbond_it2.88
c_mcangle_it2.47
c_mcbond_it1.79
c_angle_deg1.3
c_improper_angle_d0.82
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it4.04
c_scbond_it2.88
c_mcangle_it2.47
c_mcbond_it1.79
c_angle_deg1.3
c_improper_angle_d0.82
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 Atoms10567
Nucleic Acid Atoms
Solvent Atoms766
Heterogen Atoms36

Software

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