6ROZ

Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based switch motif


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.129331.7% (w/v) PEG 3350, 0.1 M HEPES, 0.233 M MgSO4
Crystal Properties
Matthews coefficientSolvent content
1.8534.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.035α = 90
b = 30.035β = 90
c = 213.113γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-FTOROIDAL FOCUSING MIRRORS2016-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00002SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.8953.281000.1820.0740.99810.413.84283-361.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.893.071001.3160.5520.764213.2

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 REPLACEMENTTHROUGHOUT3tkz2.8953.28381141899.980.243720.239430.28462RANDOM70.991
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]
-0.32-0.320.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.873
r_dihedral_angle_4_deg23.298
r_dihedral_angle_3_deg16.305
r_dihedral_angle_1_deg6.127
r_angle_refined_deg1.252
r_long_range_B_refined1.041
r_long_range_B_other1.041
r_angle_other_deg0.978
r_mcangle_it0.236
r_mcangle_other0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.873
r_dihedral_angle_4_deg23.298
r_dihedral_angle_3_deg16.305
r_dihedral_angle_1_deg6.127
r_angle_refined_deg1.252
r_long_range_B_refined1.041
r_long_range_B_other1.041
r_angle_other_deg0.978
r_mcangle_it0.236
r_mcangle_other0.236
r_scangle_other0.13
r_mcbond_other0.126
r_mcbond_it0.125
r_chiral_restr0.073
r_scbond_it0.063
r_scbond_other0.063
r_bond_refined_d0.008
r_bond_other_d0.004
r_gen_planes_refined0.004
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 Atoms1808
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing