2CJZ

crystal structure of the c472s mutant of human protein tyrosine phosphatase ptpn5 (step, striatum enriched phosphatase) in complex with phosphotyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BIJPDB ENTRY 2BIJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP150 NL SITTING DROPS, 0.1 M CACL2, 0.1 M TRIS PH 8, 20% PEG 6K, 10% ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.342α = 90
b = 64.348β = 90
c = 100.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.750.3998.50.0711.923.4376923
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)
11.71.891.60.273.072.31

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 2BIJ1.7101.0235803188898.50.1770.1750.205RANDOM12.38
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]
0.68-0.26-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.769
r_dihedral_angle_4_deg15.849
r_dihedral_angle_3_deg10.922
r_scangle_it6.32
r_dihedral_angle_1_deg5.273
r_scbond_it4.667
r_mcangle_it3.653
r_mcbond_it2.754
r_angle_refined_deg1.107
r_angle_other_deg0.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.769
r_dihedral_angle_4_deg15.849
r_dihedral_angle_3_deg10.922
r_scangle_it6.32
r_dihedral_angle_1_deg5.273
r_scbond_it4.667
r_mcangle_it3.653
r_mcbond_it2.754
r_angle_refined_deg1.107
r_angle_other_deg0.825
r_xyhbond_nbd_refined0.289
r_symmetry_vdw_other0.219
r_nbd_refined0.207
r_nbd_other0.188
r_nbtor_refined0.176
r_symmetry_hbond_refined0.166
r_nbtor_other0.081
r_symmetry_vdw_refined0.069
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms2194
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing