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Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide
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, SITTING DROP 8.5 293 0.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding.
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.626 α = 90 b = 84.72 β = 90 c = 195.68 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.55 48.92 99.6 9.2 5.2 153547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 98.8 1.2 5
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 1.55 48.92 145899 7664 99.59 0.1811 0.17907 0.1891 0.21956 0.2263 RANDOM 20.241
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] -1.25 2.12 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.446 r_dihedral_angle_4_deg 26.31 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 7.154 r_long_range_B_other 5.642 r_long_range_B_refined 5.641 r_scangle_other 3.13 r_mcangle_other 2.179 r_mcangle_it 2.178 r_scbond_it 2.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.446 r_dihedral_angle_4_deg 26.31 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 7.154 r_long_range_B_other 5.642 r_long_range_B_refined 5.641 r_scangle_other 3.13 r_mcangle_other 2.179 r_mcangle_it 2.178 r_scbond_it 2.054 r_scbond_other 2.052 r_angle_refined_deg 1.902 r_mcbond_it 1.479 r_mcbond_other 1.476 r_angle_other_deg 1.231 r_chiral_restr 0.153 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.004 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 1194 Heterogen Atoms 554
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing