7FRQ

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000217b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Crystal Properties
Matthews coefficientSolvent content
3.2962.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.465α = 90
b = 89.465β = 90
c = 106.381γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277PIXELDECTRIS PILATUS 6M2019-07-27SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96874DiamondI24

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
12.0153.1994.870.1330.1440.9957.431617
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)
12.012.0499.221.581.7210.2550.6

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 REPLACEMENTTHROUGHOUT2.0144.7730150124894.270.17130.16950.2169RANDOM46.699
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]
-0.01-0.01-0.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.405
r_dihedral_angle_4_deg23.538
r_dihedral_angle_3_deg15.857
r_dihedral_angle_1_deg6.469
r_mcangle_it4.661
r_mcbond_it3.205
r_mcbond_other3.169
r_angle_refined_deg1.461
r_angle_other_deg1.278
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.405
r_dihedral_angle_4_deg23.538
r_dihedral_angle_3_deg15.857
r_dihedral_angle_1_deg6.469
r_mcangle_it4.661
r_mcbond_it3.205
r_mcbond_other3.169
r_angle_refined_deg1.461
r_angle_other_deg1.278
r_chiral_restr0.069
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2297
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2.multiplexdata scaling
DIALSdata reduction
DIMPLEphasing