4Z9A

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529126% (w/v) PEG 5000, 0.2 M ammonium sulfate, 0.2 M MES buffer pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4649.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.75α = 90
b = 55.23β = 90
c = 97.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.459LNLSW01B-MX2

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
12.132.698.20.0859.2410699
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)
12.12.2197.30.5082.24

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 REPLACEMENTTHROUGHOUT5PNT2.128.07984679697.590.18320.179090.23511RANDOM41.696
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]
-0.45-0.180.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.888
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg6.448
r_long_range_B_refined6.413
r_long_range_B_other6.411
r_scangle_other4.204
r_mcangle_other3.294
r_mcangle_it3.288
r_scbond_it2.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.888
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg6.448
r_long_range_B_refined6.413
r_long_range_B_other6.411
r_scangle_other4.204
r_mcangle_other3.294
r_mcangle_it3.288
r_scbond_it2.813
r_scbond_other2.812
r_mcbond_it2.304
r_mcbond_other2.258
r_angle_refined_deg1.66
r_angle_other_deg0.873
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms1230
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing