X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelin-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
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.35α = 90
b = 88.35β = 90
c = 162.66γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.6232.531000.0890.0260.99915.31382423
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)
11.621.651002.0010.6290.517111

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 protein1.6231.9578148417599.920.179970.178010.21686RANDOM32.603
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]
-0.41-0.410.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.986
r_dihedral_angle_4_deg18.975
r_dihedral_angle_3_deg14.672
r_long_range_B_refined7.368
r_long_range_B_other7.335
r_dihedral_angle_1_deg6.218
r_scangle_other4.896
r_scbond_it3.287
r_scbond_other3.286
r_mcangle_it3.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.986
r_dihedral_angle_4_deg18.975
r_dihedral_angle_3_deg14.672
r_long_range_B_refined7.368
r_long_range_B_other7.335
r_dihedral_angle_1_deg6.218
r_scangle_other4.896
r_scbond_it3.287
r_scbond_other3.286
r_mcangle_it3.056
r_mcangle_other3.047
r_angle_refined_deg2.59
r_mcbond_it2.153
r_mcbond_other2.136
r_angle_other_deg1.237
r_chiral_restr0.172
r_bond_refined_d0.03
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4631
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing