3ONN

Crystal structure of 5'-nucleotidase SDT1 from saccharomyces cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528730% PEG 4000, 0.1M Tris-HCl buffer, pH 8.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K
Crystal Properties
Matthews coefficientSolvent content
2.1542.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.72α = 90
b = 77.55β = 90
c = 82.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-01-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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
11.8640.7298.50.07121.28.9225892226122
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)
1.861.9689.80.474.78.42894

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSAD1.8738.7753.582248722150114599.840.20350.20040.19760.2498
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]
0.2716-0.165-0.1066
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.018
f_angle_d1.038
f_chiral_restr0.071
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1975
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms48

Software

Software
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling