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Crystal structure of E-cadherin EC12 E89A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EDH PDB ENTRY 1EDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.25M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG 5000 monomethylether, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.63 α = 90 b = 77.122 β = 115.25 c = 71.675 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 CCD ADSC QUANTUM 4 2007-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9795 NSLS X4A
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 2.3 50 99 0.093 11.8 3 28461 28177 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1EDH 2.3 20 28177 26309 1387 98.75 0.169 0.1689 0.16578 0.1627 0.22753 0.221 RANDOM 34.417
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] 1.4 2.45 -0.19 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_4_deg 16.773 r_dihedral_angle_3_deg 14.332 r_dihedral_angle_1_deg 6.583 r_scangle_it 2.967 r_scbond_it 1.8 r_angle_refined_deg 1.48 r_mcangle_it 1.037 r_mcbond_it 0.644 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_4_deg 16.773 r_dihedral_angle_3_deg 14.332 r_dihedral_angle_1_deg 6.583 r_scangle_it 2.967 r_scbond_it 1.8 r_angle_refined_deg 1.48 r_mcangle_it 1.037 r_mcbond_it 0.644 r_nbtor_refined 0.301 r_xyhbond_nbd_refined 0.221 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.186 r_chiral_restr 0.089 r_metal_ion_refined 0.076 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3194 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 6
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling