4Z9B

Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729132% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3647.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.088α = 90
b = 54.287β = 90
c = 97.468γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2013-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.427.899.70.145516.3411.847097
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)
12.42.451000.56182.9411.58

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 REPLACEMENTTHROUGHOUT5PNT2.4127.8664132599.260.218750.214790.30148RANDOM35.003
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]
1.77-1.7-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.456
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg15.492
r_dihedral_angle_1_deg6.825
r_long_range_B_refined4.635
r_long_range_B_other4.634
r_mcangle_it2.513
r_mcangle_other2.512
r_scangle_other2.334
r_angle_refined_deg1.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.456
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg15.492
r_dihedral_angle_1_deg6.825
r_long_range_B_refined4.635
r_long_range_B_other4.634
r_mcangle_it2.513
r_mcangle_other2.512
r_scangle_other2.334
r_angle_refined_deg1.562
r_mcbond_it1.502
r_mcbond_other1.502
r_scbond_it1.393
r_scbond_other1.393
r_angle_other_deg0.89
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1249
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms11

Software

Software
Software NamePurpose
APEXdata collection
APEXdata reduction
APEXdata scaling
PHASERphasing
REFMACrefinement