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Crystal structure of E-cadherin EC12 W2A
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 8.5 293 0.1M Tris, pH 8.5, 1.3M ammonium sulfate, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.536 α = 90 b = 80.857 β = 116.84 c = 72.519 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 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 2.6 50 100 0.086 12.9 3.6 19548 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 (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 2.6 50 18549 18549 998 98.4 0.229 0.227 0.2242 0.267 0.2612 RANDOM 36.73
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] 1.96 3.23 -0.17 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_4_deg 10.115 r_dihedral_angle_1_deg 9.912 r_scangle_it 1.553 r_angle_refined_deg 0.995 r_mcangle_it 0.917 r_scbond_it 0.79 r_mcbond_it 0.488 r_chiral_restr 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_4_deg 10.115 r_dihedral_angle_1_deg 9.912 r_scangle_it 1.553 r_angle_refined_deg 0.995 r_mcangle_it 0.917 r_scbond_it 0.79 r_mcbond_it 0.488 r_chiral_restr 0.232 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other 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 157 Heterogen Atoms 6
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling