2A3K

Crystal Structure of the Human Protein Tyrosine Phosphatase, PTPN7 (HePTP, Hematopoietic Protein Tyrosine Phosphatase)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1M Tris-HCl, 2.0M ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.125α = 90
b = 80.968β = 90
c = 100.392γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9207SLSX10SA

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
12.555099.40.1281083310833
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)
12.552.6496.90.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1JLN2.5542.68103661036652299.230.221840.221840.218970.27466RANDOM29.008
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]
-4.020.153.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.519
r_dihedral_angle_4_deg19.021
r_dihedral_angle_3_deg17.276
r_dihedral_angle_1_deg6.512
r_scangle_it1.913
r_angle_refined_deg1.27
r_scbond_it1.207
r_mcangle_it0.817
r_mcbond_it0.457
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.519
r_dihedral_angle_4_deg19.021
r_dihedral_angle_3_deg17.276
r_dihedral_angle_1_deg6.512
r_scangle_it1.913
r_angle_refined_deg1.27
r_scbond_it1.207
r_mcangle_it0.817
r_mcbond_it0.457
r_nbtor_refined0.306
r_symmetry_hbond_refined0.238
r_nbd_refined0.21
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.163
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2134
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing