2I4E

Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I3UPDB ENTRY 2I3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829821% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.058α = 90
b = 71.721β = 93.31
c = 69.859γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHSi monochromator2004-02-02MSINGLE 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
11.7538.1497.10.02524.83.2597765977626.9
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)
11.751.8597.70.1357.12.58987

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 2I3U1.7538.15975659756303597.120.1850.180.1830.221RANDOM29.95
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]
0.020.52-1.21.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.2
r_dihedral_angle_4_deg17.168
r_dihedral_angle_3_deg15.364
r_dihedral_angle_1_deg6.897
r_scangle_it5.941
r_scbond_it4.018
r_mcangle_it2.824
r_mcbond_it1.856
r_angle_refined_deg1.673
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.2
r_dihedral_angle_4_deg17.168
r_dihedral_angle_3_deg15.364
r_dihedral_angle_1_deg6.897
r_scangle_it5.941
r_scbond_it4.018
r_mcangle_it2.824
r_mcbond_it1.856
r_angle_refined_deg1.673
r_nbtor_refined0.317
r_symmetry_vdw_refined0.24
r_nbd_refined0.231
r_xyhbond_nbd_refined0.17
r_symmetry_hbond_refined0.148
r_chiral_restr0.142
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4583
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms10

Software

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