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Crystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 16% PEG 3350, 100mM sodium cacodylate, 200mM ammonium fluoride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.9 α = 90 b = 96.9 β = 90 c = 165.622 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 2.2 83.92 39693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32
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 2.2 23.97 37666 2019 89.04 0.19081 0.18818 0.1862 0.23992 0.2392 RANDOM 22.463
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] -0.6 -0.3 -0.6 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 16.078 r_dihedral_angle_4_deg 14.377 r_dihedral_angle_1_deg 7.162 r_scangle_it 2.569 r_scbond_it 1.629 r_angle_refined_deg 1.468 r_mcangle_it 1.205 r_mcbond_it 0.704 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 16.078 r_dihedral_angle_4_deg 14.377 r_dihedral_angle_1_deg 7.162 r_scangle_it 2.569 r_scbond_it 1.629 r_angle_refined_deg 1.468 r_mcangle_it 1.205 r_mcbond_it 0.704 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.203 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 480 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement