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Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal substitutions)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S5E stripped of solvent and ligand molecules, used one copy of the holotoxin (1 A subunit, 5 B subunits) as the search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 Crystallization mix:
20% w/v PEG 6K
0.1 M HEPES pH 7.0
0.2 M NH4Cl
Protein storage buffer:
0.05 M Tris/HCl pH 7.5
0.2 M NaCl
0.05 M D-(+)-galactose
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.295 α = 90 b = 89.61 β = 98.186 c = 141.094 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 PILATUS 2M-F 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.6 48.9 99.9 0.18 0.196 0.076 0.995 6.6 6.7 195625 21.6
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 1.6 1.63 99.7 1 1 1 0.997 0.6 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 48.9 195625 2055 99.781 0.194 0.1932 0.203 0.2239 0.2326 23.729
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] -0.714 0.019 2.141 -1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.6 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_2_deg 8.16 r_dihedral_angle_1_deg 7.1 r_lrange_it 4.914 r_lrange_other 4.914 r_scangle_it 3.35 r_scangle_other 3.35 r_mcangle_it 2.424 r_mcangle_other 2.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.6 r_dihedral_angle_3_deg 14.264 r_dihedral_angle_2_deg 8.16 r_dihedral_angle_1_deg 7.1 r_lrange_it 4.914 r_lrange_other 4.914 r_scangle_it 3.35 r_scangle_other 3.35 r_mcangle_it 2.424 r_mcangle_other 2.424 r_scbond_it 2.094 r_scbond_other 2.094 r_mcbond_it 1.555 r_mcbond_other 1.555 r_angle_refined_deg 1.445 r_angle_other_deg 0.489 r_nbd_refined 0.211 r_symmetry_nbd_other 0.186 r_nbd_other 0.183 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.121 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11848 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building MxCuBE data collection