2C7S

Crystal structure of human protein tyrosine phosphatase kappa at 1.95A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RPMPDB ENTRY 1RPM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPSITTING DROP, 0.2M NANO3, 20% PEG3350, 10% ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
3.260

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.373α = 90
b = 91.373β = 90
c = 108.415γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.955296.30.0811.146.1328663
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0587.70.294.15.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1RPM1.9569.8431191163596.30.2010.20.218RANDOM31.75
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]
0.590.59-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_4_deg16.465
r_dihedral_angle_3_deg13.931
r_dihedral_angle_1_deg6.255
r_scangle_it2.042
r_scbond_it1.397
r_angle_refined_deg1.202
r_mcangle_it0.997
r_angle_other_deg0.864
r_mcbond_it0.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_4_deg16.465
r_dihedral_angle_3_deg13.931
r_dihedral_angle_1_deg6.255
r_scangle_it2.042
r_scbond_it1.397
r_angle_refined_deg1.202
r_mcangle_it0.997
r_angle_other_deg0.864
r_mcbond_it0.624
r_symmetry_vdw_other0.29
r_nbd_other0.192
r_nbd_refined0.189
r_nbtor_refined0.179
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.142
r_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2299
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing