3I80

Protein Tyrosine Phosphatase 1B - Transition state analog for the second catalytic step


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SUGPDB ENTRY 1SUG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277Drop: 2 uL of protein solution, 0.5 uL sucrose 30% (w/v) and 3 uL of precipitant solution (0.1 M HEPES pH 7.5, 0.2 M magnesium acetate and 18-20% polyethylene glycol 8000). Well: 500 uL of precipitant solution. The protein solution was prepared as follows: 9 uL of 50 mM of Na3VO4 and 1 uL of 50 mM of DADEYL peptide (at pH 8.5-9.0) were mixed and allowed to react for 1-1.5 hour; then, 50 uL of native PTP1B (12 mg/mL in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT) was added and the solution used immediately for crystallization. VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0960.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.84α = 90
b = 87.84β = 90
c = 103.79γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2008-09-06SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.2538.041000.0848.64.01224532245344.7
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)
2.252.3399.90.4732.24.042199

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1SUG2.2535.7131.92244122441114952.790.2010.2010.1990.235RANDOM45.377
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]
-0.669-0.6691.339
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.173
f_angle_d0.939
f_chiral_restr0.067
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2434
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms31

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction