2BGD

Structure-based design of Protein Tyrosine Phosphatase-1B Inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.50
Crystal Properties
Matthews coefficientSolvent content
3.2762.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.908α = 90
b = 88.908β = 90
c = 104.548γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002002-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.427.4298.60.0611.22.89105241
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)
12.42.5396.30.174.492.79

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.429.111787696398.40.1660.1640.2RANDOM23.17
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]
0.140.070.14-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.91
r_scangle_it3.204
r_scbond_it1.88
r_angle_refined_deg1.413
r_mcangle_it1.104
r_angle_other_deg0.822
r_mcbond_it0.538
r_symmetry_vdw_other0.246
r_nbd_other0.24
r_nbd_refined0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.91
r_scangle_it3.204
r_scbond_it1.88
r_angle_refined_deg1.413
r_mcangle_it1.104
r_angle_other_deg0.822
r_mcbond_it0.538
r_symmetry_vdw_other0.246
r_nbd_other0.24
r_nbd_refined0.205
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.135
r_symmetry_vdw_refined0.104
r_nbtor_other0.084
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2398
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing