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Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M GlyGly/AMPD pH 8.5, 0.03M of each Lithium sulfate, Sodium sulfate, and Potassium sulfate. Tray 307437a10: puck ckt8-9.
Crystal Properties Matthews coefficient Solvent content 3.04 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.17 α = 90 b = 142.17 β = 90 c = 90.32 γ = 120
Symmetry Space Group P 31 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 RAYONIX MX-300 Beryllium Lenses 2019-07-18 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 2.65 46.54 99.9 0.061 0.065 0.999 24.68 8.734 30906 60.262
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 2.65 2.72 100 0.595 0.631 0.92 3.56 8.984
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2o72 2.65 46.54 1.35 30872 1542 99.95 0.1961 0.194 0.1978 0.2358 0.2387 74.6742
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 4723 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing