2BIJ

Crystal structure of the human protein tyrosine phosphatase PTPN5 (STEP, striatum enriched enriched Phosphatase)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JLNPDB ENTRY 1JLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN SOLUTION: 10 MG/ML PTPN5, 50 MM HEPES PH 7.5, 200 MM NACL, 10 MM DTT PRECIPITANT: 25% PEG3350, 0.2 M LI2SO4, 100 MM BIS-TR-S PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.808α = 90
b = 64.318β = 90
c = 101.077γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMULTILAYER MIRRORS2004-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.0539.74950.0911.144.7208253
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)
12.052.15970.373.053.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1JLN2.0554.2319570104794.20.2150.2120.264RANDOM36.21
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]
2.71-1.34-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_3_deg15.933
r_dihedral_angle_4_deg15.143
r_dihedral_angle_1_deg6.417
r_scangle_it2.985
r_scbond_it1.889
r_angle_refined_deg1.484
r_mcangle_it1.241
r_angle_other_deg0.838
r_mcbond_it0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_3_deg15.933
r_dihedral_angle_4_deg15.143
r_dihedral_angle_1_deg6.417
r_scangle_it2.985
r_scbond_it1.889
r_angle_refined_deg1.484
r_mcangle_it1.241
r_angle_other_deg0.838
r_mcbond_it0.772
r_symmetry_vdw_refined0.33
r_nbd_refined0.214
r_symmetry_vdw_other0.186
r_nbd_other0.181
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.144
r_chiral_restr0.085
r_nbtor_other0.084
r_symmetry_hbond_refined0.022
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2265
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing