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Cholera toxin classical B-pentamer in complex with fucosyl-GM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293.15 0.1 M Bicine-Tris, 6% PEG1000, 6% PEG3350, 6% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.626 α = 90 b = 74.137 β = 105.59 c = 111.245 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 PIXEL DECTRIS EIGER X 16M 2018-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.980802 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.6 44.32 98.4 0.176 4.9 2.6 150674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.964 0.449
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 5ELB 1.6 44.32 143082 7592 98.19 0.18517 0.18364 0.1967 0.21414 0.2255 RANDOM 13.369
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] -0.01 0.23 0.67 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.836 r_dihedral_angle_4_deg 20.872 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_1_deg 13.303 r_long_range_B_refined 3.862 r_long_range_B_other 3.862 r_angle_refined_deg 1.831 r_scangle_other 1.05 r_angle_other_deg 0.998 r_mcangle_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.836 r_dihedral_angle_4_deg 20.872 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_1_deg 13.303 r_long_range_B_refined 3.862 r_long_range_B_other 3.862 r_angle_refined_deg 1.831 r_scangle_other 1.05 r_angle_other_deg 0.998 r_mcangle_it 0.812 r_mcangle_other 0.812 r_scbond_it 0.66 r_scbond_other 0.66 r_mcbond_it 0.481 r_mcbond_other 0.48 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8140 Nucleic Acid Atoms Solvent Atoms 797 Heterogen Atoms 922
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing