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Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6S 1o6s 4zmt experimental model PDB 4ZMT 1o6s 4zmt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Ammonium acetate
45% MPD
Crystal Properties Matthews coefficient Solvent content 3.53 65.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.35 α = 101.48 b = 69.58 β = 97.77 c = 72.49 γ = 105.99
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 315 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.91 34.8 92.3 0.088 0.996 8.8 3.8 71483
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.95 92.1 0.76 0.837 2.1 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1o6s 4zmt 1.91 34.8 68640 2835 92.31 0.1776 0.1763 0.1836 0.2097 0.214 RANDOM 26.343
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] -1.5 0.41 -0.36 1.79 0.55 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.307 r_dihedral_angle_2_deg 12.258 r_dihedral_angle_1_deg 7.505 r_angle_refined_deg 1.371 r_angle_other_deg 0.458 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5136 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling MOLREP phasing