2HC2

Engineered protein tyrosine phosphatase beta catalytic domain


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8529821% PEG 8000, 200 mM MgCl2, 1% BME, 0.1% BOG, 1mM DTT, 80 mM Na Citrate, pH 7.85, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.314α = 90
b = 70.775β = 92.52
c = 49.846γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCH2006-02-02MSINGLE 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
11.433.6792.50.02820.22.64839748397
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)
1.41.569.40.214.871.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HC11.433.674839745933246492.510.145710.143910.17892RANDOM19.055
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]
0.670.05-0.32-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_sphericity_free16.373
r_dihedral_angle_4_deg15.582
r_dihedral_angle_3_deg14.775
r_sphericity_bonded10.465
r_scangle_it6.959
r_dihedral_angle_1_deg6.896
r_scbond_it5.308
r_mcangle_it4.138
r_rigid_bond_restr3.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_sphericity_free16.373
r_dihedral_angle_4_deg15.582
r_dihedral_angle_3_deg14.775
r_sphericity_bonded10.465
r_scangle_it6.959
r_dihedral_angle_1_deg6.896
r_scbond_it5.308
r_mcangle_it4.138
r_rigid_bond_restr3.487
r_mcbond_it3.024
r_angle_refined_deg1.206
r_symmetry_vdw_refined0.375
r_nbtor_refined0.319
r_nbd_refined0.26
r_xyhbond_nbd_refined0.206
r_symmetry_hbond_refined0.156
r_chiral_restr0.102
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2488
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms3

Software

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