8G67

Wildtype PTP1b in complex with DES4884


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house structure of same protein

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.2278Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2; Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.3848.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.57α = 90
b = 89.57β = 90
c = 164.31γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.5343.2199.60.0790.0240.99916.712100903
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.5799.91.9450.6940.551.18.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTin-house structure of same protein1.5343.2195742503599.580.157930.15440.22259RANDOM33.014
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]
1.291.29-2.58
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free62.009
r_dihedral_angle_2_deg35.291
r_sphericity_bonded28.448
r_dihedral_angle_4_deg17.447
r_dihedral_angle_3_deg13.729
r_long_range_B_refined10.523
r_long_range_B_other10.522
r_scangle_other9.97
r_scbond_it8.782
r_scbond_other8.782
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free62.009
r_dihedral_angle_2_deg35.291
r_sphericity_bonded28.448
r_dihedral_angle_4_deg17.447
r_dihedral_angle_3_deg13.729
r_long_range_B_refined10.523
r_long_range_B_other10.522
r_scangle_other9.97
r_scbond_it8.782
r_scbond_other8.782
r_mcangle_it6.869
r_mcangle_other6.869
r_dihedral_angle_1_deg6.251
r_mcbond_it5.639
r_mcbond_other5.638
r_rigid_bond_restr5.521
r_angle_refined_deg1.855
r_angle_other_deg1.033
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4632
Nucleic Acid Atoms
Solvent Atoms540
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing