3N8I | pdb_00003n8i

Crystal structure of the A isoform of human cytoplasmic protein tyrosine phosphatase (HCPTP-A) in complex with 1-naphtylacetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5PNT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529822.5% PEG 3350, 0.1M TRIS pH 7.5, 10mM 1-naphthylacetic acid, 2% isopropanol, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.46α = 90
b = 56.09β = 90
c = 95.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDSI(111) double crystal monochromator2009-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.968APS23-ID-D

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
11.55099.030.12715.0212.227538272701122.919.291
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)
11.51.5596.20.3894.715.92738

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5PNT1.532.4612753727270146499.030.1750.1740.18230.2030.2145RANDOM19.291
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]
-0.130.19-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.692
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg5.336
r_sphericity_free3.017
r_scangle_it2.933
r_sphericity_bonded2.152
r_scbond_it1.961
r_mcangle_it1.362
r_angle_refined_deg1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.692
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg5.336
r_sphericity_free3.017
r_scangle_it2.933
r_sphericity_bonded2.152
r_scbond_it1.961
r_mcangle_it1.362
r_angle_refined_deg1.164
r_rigid_bond_restr1.04
r_mcbond_it0.794
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1229
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms14

Software

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