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Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 50 mM
Crystal Properties Matthews coefficient Solvent content 3.46 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.446 α = 90 b = 76.417 β = 109.98 c = 73.02 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2014-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.87 42.66 86.4 0.045 8.4 2 48085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 58.5 0.253 2.2 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2O72 1.92 42.65 44649 2350 98.7 0.1941 0.19277 0.2 0.2189 0.2255 RANDOM 46.422
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] 3.76 1.52 -1.73 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.087 r_dihedral_angle_4_deg 20.586 r_dihedral_angle_3_deg 14.71 r_long_range_B_refined 14.124 r_long_range_B_other 11.173 r_scangle_other 9.266 r_dihedral_angle_1_deg 9.152 r_mcangle_other 6.837 r_mcangle_it 6.836 r_scbond_it 6.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.087 r_dihedral_angle_4_deg 20.586 r_dihedral_angle_3_deg 14.71 r_long_range_B_refined 14.124 r_long_range_B_other 11.173 r_scangle_other 9.266 r_dihedral_angle_1_deg 9.152 r_mcangle_other 6.837 r_mcangle_it 6.836 r_scbond_it 6.776 r_scbond_other 6.756 r_mcbond_it 5.309 r_mcbond_other 5.307 r_angle_refined_deg 0.507 r_angle_other_deg 0.455 r_chiral_restr 0.043 r_gen_planes_refined 0.016 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3180 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing XDS data reduction