☰ Navigation Tabs
Cholera toxin El Tor B-pentamer in complex with Lewis-y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Bicine-Tris, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.667 α = 90 b = 80.916 β = 96.07 c = 95.77 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 2M 2014-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 47.62 94.4 0.064 9.2 2.6 146071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 85.2 0.625 1.34 2.4
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 3CHB 1.5 47.62 138740 7329 94.45 0.22332 0.22141 0.2243 0.25956 0.2596 RANDOM 19.088
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] -8.77 1.63 -0.74 9.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.852 r_dihedral_angle_4_deg 24.784 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 9.34 r_long_range_B_refined 4.231 r_long_range_B_other 4.231 r_scangle_other 2.508 r_mcangle_it 2.081 r_mcangle_other 2.081 r_angle_refined_deg 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.852 r_dihedral_angle_4_deg 24.784 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 9.34 r_long_range_B_refined 4.231 r_long_range_B_other 4.231 r_scangle_other 2.508 r_mcangle_it 2.081 r_mcangle_other 2.081 r_angle_refined_deg 1.956 r_scbond_it 1.653 r_scbond_other 1.653 r_mcbond_it 1.385 r_mcbond_other 1.385 r_angle_other_deg 1.181 r_chiral_restr 0.151 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 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 8170 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 545
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing