2BV5

CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 AT 1.8A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BIJPDB ENTRY 2BIJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPSITTING DROP, 25% PEG3350, 0.2M LI2SO4, 100MM BIS TRIS PROPANE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.550.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.957α = 90
b = 64.01β = 90
c = 136.149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.839.9698.70.0612.94.9328772.5
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)
11.81.995.40.372.52.5

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 2BIJ1.868.0431160166598.70.1660.1640.201RANDOM17.76
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]
0.36-0.410.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg12.622
r_dihedral_angle_3_deg12.096
r_dihedral_angle_1_deg5.503
r_scangle_it2.662
r_scbond_it1.773
r_angle_refined_deg1.322
r_mcangle_it1.122
r_angle_other_deg0.783
r_mcbond_it0.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg12.622
r_dihedral_angle_3_deg12.096
r_dihedral_angle_1_deg5.503
r_scangle_it2.662
r_scbond_it1.773
r_angle_refined_deg1.322
r_mcangle_it1.122
r_angle_other_deg0.783
r_mcbond_it0.715
r_symmetry_vdw_other0.304
r_symmetry_vdw_refined0.27
r_nbd_refined0.253
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.19
r_nbd_other0.183
r_nbtor_refined0.178
r_nbtor_other0.082
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms2239
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing