7FRR

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434906


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
3.2962.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.527α = 90
b = 89.527β = 90
c = 106.242γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277PIXELDECTRIS PILATUS 6M2019-07-22SINGLE 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
11.8362.6399.990.1510.1620.9878.643932
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)
11.831.861002.9763.1920.2990.5

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 REPLACEMENTTHROUGHOUT1.8362.6342135172799.90.1770.1750.214RANDOM41.83
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]
-0.01-0.01-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.416
r_dihedral_angle_4_deg18.704
r_dihedral_angle_3_deg16.424
r_dihedral_angle_1_deg6.132
r_mcangle_it4.067
r_mcbond_other3.533
r_mcbond_it3.531
r_angle_refined_deg1.512
r_angle_other_deg1.318
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.416
r_dihedral_angle_4_deg18.704
r_dihedral_angle_3_deg16.424
r_dihedral_angle_1_deg6.132
r_mcangle_it4.067
r_mcbond_other3.533
r_mcbond_it3.531
r_angle_refined_deg1.512
r_angle_other_deg1.318
r_chiral_restr0.075
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2427
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms20

Software

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