7KEN

Protein Tyrosine Phosphatase 1B, D289A mutant, apo state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B90PDB entry 6B90

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277100 mM HEPES, 200 mM magnesium acetate, 14% PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.1761.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.314α = 90
b = 88.314β = 90
c = 104.155γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97741ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.876.481000.1780.1870.0560.9976.210.84098923.27
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831000.3150.3

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 6B901.876.4840989213998.030.205610.203510.24369RANDOM38.766
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]
0.230.120.23-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.349
r_dihedral_angle_4_deg15.843
r_dihedral_angle_3_deg15.198
r_long_range_B_other11.235
r_long_range_B_refined11.207
r_scangle_other9.034
r_mcangle_it7.273
r_mcangle_other7.272
r_scbond_it6.579
r_scbond_other6.576
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.349
r_dihedral_angle_4_deg15.843
r_dihedral_angle_3_deg15.198
r_long_range_B_other11.235
r_long_range_B_refined11.207
r_scangle_other9.034
r_mcangle_it7.273
r_mcangle_other7.272
r_scbond_it6.579
r_scbond_other6.576
r_dihedral_angle_1_deg6.31
r_mcbond_it5.401
r_mcbond_other5.38
r_angle_refined_deg1.418
r_angle_other_deg1.139
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2431
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing