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Engineered higher-order assembly of Cholera Toxin B subunits via the addition of C-terminal parallel coiled-coiled domains
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 Hampton Crystal Screen 2 condition #43:
0.2 M Ammonium Phosphate monobasic, 0.1 M Tris (pH 8.5), 50% v/v (+/-)-2-Methyl-2,4-pentanediol.
Crystal Properties Matthews coefficient Solvent content 3.54 65.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.16 α = 90 b = 179.16 β = 90 c = 192.02 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 100 PIXEL DECTRIS PILATUS 6M 2014-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.45 37.28 100 0.092 0.097 0.03 0.999 19 10.2 127892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 100 0.698 0.744 0.346 0.864 3.2 8.4
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 2.45 37.28 121547 6304 99.96 0.19639 0.19548 0.1965 0.21378 0.213 RANDOM 55.917
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] 0.97 0.48 0.97 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.244 r_dihedral_angle_4_deg 26.331 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 15.048 r_long_range_B_refined 6.508 r_long_range_B_other 6.508 r_scangle_other 3.221 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 2.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.244 r_dihedral_angle_4_deg 26.331 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 15.048 r_long_range_B_refined 6.508 r_long_range_B_other 6.508 r_scangle_other 3.221 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 2.157 r_scbond_other 2.157 r_angle_refined_deg 1.794 r_mcbond_it 1.442 r_mcbond_other 1.441 r_angle_other_deg 1.367 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 17187 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 247
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling MOLREP phasing