4Z99

Crystal structure of the apo Low Molecular Weight Protein Tyrosine Phosphatase isoform A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729127% (w/v) PEG 2000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.667α = 90
b = 54.157β = 90
c = 100.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2013-04-26MSINGLE 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
12.354.1699.70.22627.438.578392
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)
12.32.351000.62127.94

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 REPLACEMENTTHROUGHOUT5PNT2.336.75796738599.680.194670.190480.28682RANDOM25.027
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]
-1.261.41-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.479
r_dihedral_angle_4_deg21.342
r_dihedral_angle_3_deg13.601
r_dihedral_angle_1_deg7.22
r_long_range_B_refined4.868
r_long_range_B_other4.634
r_scangle_other2.205
r_mcangle_other2.057
r_mcangle_it2.056
r_angle_refined_deg1.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.479
r_dihedral_angle_4_deg21.342
r_dihedral_angle_3_deg13.601
r_dihedral_angle_1_deg7.22
r_long_range_B_refined4.868
r_long_range_B_other4.634
r_scangle_other2.205
r_mcangle_other2.057
r_mcangle_it2.056
r_angle_refined_deg1.487
r_scbond_it1.323
r_scbond_other1.323
r_mcbond_it1.228
r_mcbond_other1.223
r_angle_other_deg0.88
r_chiral_restr0.079
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 Atoms1294
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata reduction
APEXdata scaling
PHASERphasing
APEXdata collection