2H04

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 (WITH MODIFICATIONS)

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
1.9637.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.803α = 90
b = 70.12β = 90
c = 90.722γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-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
12.334.8699.60.098.883.8132481324822
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)
2.32.498.30.372.833.11529

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 1RPM (WITH MODIFICATIONS)2.334.86132071320764999.650.1720.170.1690.238RANDOM16.455
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]
0.12-0.230.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.525
r_dihedral_angle_3_deg19.278
r_dihedral_angle_4_deg18.391
r_dihedral_angle_1_deg8.347
r_scangle_it6.463
r_scbond_it4.613
r_mcangle_it2.793
r_angle_refined_deg2.155
r_mcbond_it1.702
r_symmetry_hbond_refined0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.525
r_dihedral_angle_3_deg19.278
r_dihedral_angle_4_deg18.391
r_dihedral_angle_1_deg8.347
r_scangle_it6.463
r_scbond_it4.613
r_mcangle_it2.793
r_angle_refined_deg2.155
r_mcbond_it1.702
r_symmetry_hbond_refined0.329
r_nbtor_refined0.319
r_symmetry_vdw_refined0.257
r_nbd_refined0.222
r_xyhbond_nbd_refined0.193
r_chiral_restr0.145
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2300
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms32

Software

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