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crystal structure of E-cadherin EC1-2 P5A P6A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FF5 PDB ENTRY 1FF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10% PEG8000, 10% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.4 72.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.185 α = 90 b = 92.583 β = 92.26 c = 79.465 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 2008-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9793 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 98.9 74512 73693 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 (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 1FF5 1.8 44.7 73693 69888 3712 98.81 0.16246 0.16162 0.176 0.17805 0.1872 RANDOM 27.787
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] -0.34 -0.39 0.36 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 13.231 r_dihedral_angle_1_deg 6.405 r_scangle_it 3.492 r_scbond_it 2.02 r_angle_refined_deg 1.324 r_mcangle_it 1.146 r_mcbond_it 0.596 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 13.231 r_dihedral_angle_1_deg 6.405 r_scangle_it 3.492 r_scbond_it 2.02 r_angle_refined_deg 1.324 r_mcangle_it 1.146 r_mcbond_it 0.596 r_nbtor_refined 0.301 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.171 r_chiral_restr 0.09 r_metal_ion_refined 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 3264 Nucleic Acid Atoms Solvent Atoms 903 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling