2H02

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 1RPMPDB ENTRY 1RPM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829821% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.144α = 90
b = 71.724β = 93.41
c = 70.297γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-01-01MSINGLE 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
12.330950.04515.692.3320023200231.1
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)
12.152.2568.70.283.761.62904

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 1RPM2.3302735327353137999.240.1920.190.1890.244RANDOM29.586
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]
1.3-0.21-0.55-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.432
r_dihedral_angle_4_deg21.923
r_dihedral_angle_3_deg19.167
r_dihedral_angle_1_deg8.779
r_scangle_it6.507
r_scbond_it4.66
r_mcangle_it3.114
r_angle_refined_deg2.162
r_mcbond_it2.041
r_symmetry_hbond_refined0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.432
r_dihedral_angle_4_deg21.923
r_dihedral_angle_3_deg19.167
r_dihedral_angle_1_deg8.779
r_scangle_it6.507
r_scbond_it4.66
r_mcangle_it3.114
r_angle_refined_deg2.162
r_mcbond_it2.041
r_symmetry_hbond_refined0.772
r_symmetry_vdw_refined0.448
r_nbtor_refined0.327
r_nbd_refined0.256
r_xyhbond_nbd_refined0.186
r_chiral_restr0.162
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4584
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data scaling
AMoREphasing