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Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZT1
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 80 mM
Crystal Properties Matthews coefficient Solvent content 3.44 64.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.579 α = 90 b = 76.835 β = 111.14 c = 72.772 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 2014-12-16 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 2.13 48.82 98.7 0.129 7.3 6 33775
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 2.13 2.25 93.5 0.123 0.6 5.3
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 4ZT1 2.13 42.26 32085 1689 97.01 0.18735 0.18515 0.194 0.22951 0.2347 RANDOM 47.401
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] 3.53 2.31 -3.34 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.699 r_dihedral_angle_4_deg 16.463 r_dihedral_angle_3_deg 15.728 r_long_range_B_refined 12.4 r_long_range_B_other 12.399 r_scangle_other 10.328 r_dihedral_angle_1_deg 9.214 r_scbond_it 7.542 r_scbond_other 7.54 r_mcangle_other 6.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.699 r_dihedral_angle_4_deg 16.463 r_dihedral_angle_3_deg 15.728 r_long_range_B_refined 12.4 r_long_range_B_other 12.399 r_scangle_other 10.328 r_dihedral_angle_1_deg 9.214 r_scbond_it 7.542 r_scbond_other 7.54 r_mcangle_other 6.195 r_mcangle_it 6.18 r_mcbond_it 4.881 r_mcbond_other 4.858 r_angle_refined_deg 0.487 r_angle_other_deg 0.436 r_chiral_restr 0.041 r_gen_planes_refined 0.016 r_bond_refined_d 0.003 r_gen_planes_other 0.002 r_bond_other_d 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 3196 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing XDS data reduction