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Crystal Structure Analysis of human E-cadherin (1-213)
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 7.5 277 10% PEG 8000, 0.2M calcium chloride, 5% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.38 63.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.341 α = 90 b = 41.077 β = 111.15 c = 59.542 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2003-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0000 APS 19-ID
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 39.1 98 0.073 9.3 6.8 21390 20837 33
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) 2 2.03 77.8 0.323 2.5 2.2 813
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EDH 2 39.1 21258 20836 1068 98.02 0.226 0.193 0.191 0.234 0.2411 RANDOM 19.055
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] -0.61 -0.23 0.56 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.17 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.347 r_scbond_it 2.262 r_angle_refined_deg 1.445 r_mcangle_it 1.323 r_mcbond_it 0.937 r_angle_other_deg 0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.17 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 13.981 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.347 r_scbond_it 2.262 r_angle_refined_deg 1.445 r_mcangle_it 1.323 r_mcbond_it 0.937 r_angle_other_deg 0.917 r_symmetry_vdw_other 0.221 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.204 r_mcbond_other 0.204 r_nbd_other 0.2 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.125 r_symmetry_vdw_refined 0.122 r_chiral_restr 0.089 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1627 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction