5OKN

Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M Bis-Tris propane, pH 7.0, 0.4 M KSCN, 20% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.065α = 90
b = 177.143β = 90
c = 177.371γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.872600ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6549.171000.0550.99613.49119204
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.71000.4670.72.28.9

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 REPLACEMENTTHROUGHOUT2.6549.17119204637099.940.207960.2060.24463RANDOM60.007
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]
1.5-1.11-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.461
r_dihedral_angle_4_deg16.996
r_dihedral_angle_3_deg13.247
r_dihedral_angle_1_deg6.279
r_long_range_B_refined4.607
r_long_range_B_other4.607
r_mcangle_it2.422
r_mcangle_other2.422
r_angle_other_deg2.02
r_scangle_other1.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.461
r_dihedral_angle_4_deg16.996
r_dihedral_angle_3_deg13.247
r_dihedral_angle_1_deg6.279
r_long_range_B_refined4.607
r_long_range_B_other4.607
r_mcangle_it2.422
r_mcangle_other2.422
r_angle_other_deg2.02
r_scangle_other1.849
r_mcbond_it1.321
r_mcbond_other1.321
r_angle_refined_deg1.267
r_scbond_it0.996
r_scbond_other0.996
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms27549
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing