8G68

Wildtype PTP1b in complex with DES5742


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
2.2645.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.99α = 90
b = 87.99β = 90
c = 162.17γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.8277.3499.80.1260.0380.99811.811.757775
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)
11.821.8699.11.9720.6150.5211.410.7

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 protein1.8277.3454693299699.720.205790.203160.25441RANDOM37.002
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]
-2.07-2.074.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.175
r_dihedral_angle_4_deg19.758
r_dihedral_angle_3_deg15.059
r_long_range_B_refined8.438
r_long_range_B_other8.437
r_scangle_other6.461
r_dihedral_angle_1_deg6.352
r_mcangle_it4.738
r_mcangle_other4.737
r_scbond_it4.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.175
r_dihedral_angle_4_deg19.758
r_dihedral_angle_3_deg15.059
r_long_range_B_refined8.438
r_long_range_B_other8.437
r_scangle_other6.461
r_dihedral_angle_1_deg6.352
r_mcangle_it4.738
r_mcangle_other4.737
r_scbond_it4.3
r_scbond_other4.299
r_mcbond_other3.478
r_mcbond_it3.477
r_angle_refined_deg1.864
r_angle_other_deg1.072
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4682
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing