2I4H

Structural studies of protein tyrosine phosphatase beta catalytic domain co-crystallized with a sulfamic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HC1PDB ENTRY 2HC1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.129820% PEG 8000, 220 mM MgCl2, 80 mM NH4OAc, 1% BME, 0.1% BOG, 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9637.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.313α = 90
b = 38.795β = 104.94
c = 66.983γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHSi monochromator2005-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.1527.3799.50.06312.484157991579921.36
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)
12.152.2597.20.1875.264.22150

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2HC12.1527.37157991579979199.550.1730.170.1690.246RANDOM15.737
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]
1.340.19-0.4-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_3_deg17.205
r_dihedral_angle_4_deg12.007
r_dihedral_angle_1_deg7.925
r_scangle_it6.16
r_scbond_it4.273
r_mcangle_it2.56
r_angle_refined_deg1.843
r_mcbond_it1.632
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_3_deg17.205
r_dihedral_angle_4_deg12.007
r_dihedral_angle_1_deg7.925
r_scangle_it6.16
r_scbond_it4.273
r_mcangle_it2.56
r_angle_refined_deg1.843
r_mcbond_it1.632
r_nbtor_refined0.315
r_symmetry_hbond_refined0.285
r_symmetry_vdw_refined0.251
r_nbd_refined0.223
r_xyhbond_nbd_refined0.181
r_chiral_restr0.158
r_symmetry_metal_ion_refined0.018
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_metal_ion_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2294
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing