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Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O72 2o72, 4web experimental model PDB 4WEB 2o72, 4web
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M HEPES/ NaOH, pH = 7.0. The crystal was cryoprotected with 20% ethylene glycol. Tray: 299140h12, puck: qxp2-3
Crystal Properties Matthews coefficient Solvent content 3.64 66.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.68 α = 90 b = 77.47 β = 92.91 c = 110.94 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 MARMOSAIC 300 mm CCD Beryllium Lenses 2018-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.2 40.091 99.9 0.082 0.094 0.997 13.4 4.19 52838 31.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.9 0.587 0.672 0.784 2.6 4.246
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2o72, 4web 2.2 40.091 1.35 52833 2648 99.92 0.1644 0.1626 0.1644 0.197 0.199 Random selection 36.399
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4849 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction