8G65

Wildtype PTP1b in complex with DES4799


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house structure of same protein

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.2278Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2; Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.3948.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.44α = 90
b = 89.44β = 90
c = 165.76γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.4582.8899.80.0860.0270.99915.811.411914914.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4999.81.7060.7030.5271.27.7

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 REPLACEMENTTHROUGHOUTin-house structure of same protein1.4563.32113016600399.780.137090.134380.18836RANDOM24.011
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]
0.880.88-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_sphericity_free29.27
r_dihedral_angle_4_deg20.331
r_sphericity_bonded19.291
r_dihedral_angle_3_deg14.229
r_scangle_other6.269
r_long_range_B_refined6.191
r_long_range_B_other6.19
r_dihedral_angle_1_deg5.948
r_rigid_bond_restr5.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_sphericity_free29.27
r_dihedral_angle_4_deg20.331
r_sphericity_bonded19.291
r_dihedral_angle_3_deg14.229
r_scangle_other6.269
r_long_range_B_refined6.191
r_long_range_B_other6.19
r_dihedral_angle_1_deg5.948
r_rigid_bond_restr5.364
r_scbond_it5.333
r_scbond_other5.332
r_mcangle_it4.056
r_mcangle_other4.055
r_mcbond_it3.416
r_mcbond_other3.416
r_angle_refined_deg2.375
r_angle_other_deg1.264
r_chiral_restr0.157
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4751
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing