5OKM

Crystal structure of human SHIP2 Phosphatase-C2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NR8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.1 M BisTris propane pH 7, 0.2 M NaNO3, 20% PEG 3350, 0.025% CH2Cl2, 2 mM TCEP
Crystal Properties
Matthews coefficientSolvent content
2.5451.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.037α = 90
b = 175.836β = 90
c = 176.893γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.9648.971000.0330.99914.86.8287002
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)
11.961.991000.3680.7432.16.7

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 REPLACEMENTTHROUGHOUT3NR81.9648.962870021518099.970.180910.17950.2075RANDOM45.654
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]
-1.12-0.151.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.215
r_dihedral_angle_4_deg19.696
r_dihedral_angle_3_deg13.663
r_dihedral_angle_1_deg6.198
r_long_range_B_refined5.622
r_long_range_B_other5.614
r_mcangle_it2.42
r_mcangle_other2.42
r_scangle_other2.362
r_mcbond_it1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.215
r_dihedral_angle_4_deg19.696
r_dihedral_angle_3_deg13.663
r_dihedral_angle_1_deg6.198
r_long_range_B_refined5.622
r_long_range_B_other5.614
r_mcangle_it2.42
r_mcangle_other2.42
r_scangle_other2.362
r_mcbond_it1.38
r_mcbond_other1.38
r_scbond_it1.346
r_scbond_other1.346
r_angle_refined_deg1.306
r_angle_other_deg1.241
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms28047
Nucleic Acid Atoms
Solvent Atoms1564
Heterogen Atoms225

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing