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Crystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 16% PEG 3350, 100mM sodium cacodylate, pH 6.2, 200mM ammonium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.253 α = 90 b = 97.253 β = 90 c = 163.52 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.1 84.22 45181
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 29.67 40527 2177 83.79 0.21338 0.21079 0.2107 0.2615 0.2615 RANDOM 23.623
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] -1.04 -0.52 -1.04 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.821 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_4_deg 7.757 r_dihedral_angle_1_deg 5.97 r_angle_refined_deg 1.538 r_scangle_it 1.015 r_scbond_it 0.589 r_mcangle_it 0.535 r_mcbond_it 0.304 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.821 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_4_deg 7.757 r_dihedral_angle_1_deg 5.97 r_angle_refined_deg 1.538 r_scangle_it 1.015 r_scbond_it 0.589 r_mcangle_it 0.535 r_mcbond_it 0.304 r_nbtor_refined 0.301 r_chiral_restr 0.217 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_refined 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 4532 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement