7GTE

PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000646b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Crystal Properties
Matthews coefficientSolvent content
3.3863.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.413α = 90
b = 90.413β = 90
c = 107.001γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-25SINGLE 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)Rrim 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
11.963.18999.70.0630.0710.99914.0976758-344.393
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92.0299.31.3511.5090.5411.07

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.963.1937872154897.860.1980.19670.2307RANDOM45.513
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]
0.430.220.43-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg18.71
r_dihedral_angle_3_deg16.067
r_dihedral_angle_1_deg6.77
r_mcangle_it4.9
r_mcbond_it4.36
r_mcbond_other4.333
r_angle_refined_deg1.614
r_angle_other_deg1.346
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.354
r_dihedral_angle_4_deg18.71
r_dihedral_angle_3_deg16.067
r_dihedral_angle_1_deg6.77
r_mcangle_it4.9
r_mcbond_it4.36
r_mcbond_other4.333
r_angle_refined_deg1.614
r_angle_other_deg1.346
r_chiral_restr0.089
r_bond_refined_d0.026
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction