☰ Navigation Tabs
Cholera toxin classical B-pentamer in complex with fucose
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, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.
Crystal Properties Matthews coefficient Solvent content 2.08 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.785 α = 90 b = 100.543 β = 117 c = 93.012 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 2018-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.979531 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 1.95 47.42 97.7 0.149 6.2 2.7 184186 67464
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 1.95 2 98.5 1.251 0.41
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 1.95 47.42 64017 3442 97.51 0.18921 0.18661 0.1968 0.23743 0.249 RANDOM 30.418
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] 0.16 -0.16 0.2 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 29.213 r_dihedral_angle_3_deg 15.458 r_dihedral_angle_1_deg 8.145 r_long_range_B_refined 3.432 r_long_range_B_other 3.432 r_angle_refined_deg 1.679 r_scangle_other 1.656 r_mcangle_it 1.52 r_mcangle_other 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 29.213 r_dihedral_angle_3_deg 15.458 r_dihedral_angle_1_deg 8.145 r_long_range_B_refined 3.432 r_long_range_B_other 3.432 r_angle_refined_deg 1.679 r_scangle_other 1.656 r_mcangle_it 1.52 r_mcangle_other 1.52 r_scbond_it 1.05 r_scbond_other 1.05 r_mcbond_it 0.956 r_mcbond_other 0.956 r_angle_other_deg 0.929 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 8131 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing