4ZT1

Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 50 mM
Crystal Properties
Matthews coefficientSolvent content
3.4664.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.446α = 90
b = 76.417β = 109.98
c = 73.02γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
11.8742.6686.40.0458.4248085
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)
11.871.9758.50.2532.21.8

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 REPLACEMENTTHROUGHOUT2O721.9242.6544649235098.70.19410.192770.2189RANDOM46.422
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]
3.761.52-1.73-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.087
r_dihedral_angle_4_deg20.586
r_dihedral_angle_3_deg14.71
r_long_range_B_refined14.124
r_long_range_B_other11.173
r_scangle_other9.266
r_dihedral_angle_1_deg9.152
r_mcangle_other6.837
r_mcangle_it6.836
r_scbond_it6.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.087
r_dihedral_angle_4_deg20.586
r_dihedral_angle_3_deg14.71
r_long_range_B_refined14.124
r_long_range_B_other11.173
r_scangle_other9.266
r_dihedral_angle_1_deg9.152
r_mcangle_other6.837
r_mcangle_it6.836
r_scbond_it6.776
r_scbond_other6.756
r_mcbond_it5.309
r_mcbond_other5.307
r_angle_refined_deg0.507
r_angle_other_deg0.455
r_chiral_restr0.043
r_gen_planes_refined0.016
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3180
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
XDSdata reduction