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Cholera holotoxin (wildtype)
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 7.4 293.15 Crystallization mix:
0.125 M Magnesium acetate
24% PEG 3350
300 mM galactose (in protein storage buffer)
Protein storage buffer:
50 mM Tris pH 7.4
200 mM NaCl
1 mM EDTA
3 mM sodium azide
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.659 α = 90 b = 108.128 β = 95.958 c = 124.765 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 EIGER2 X 9M 2021-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
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 2.3 124.091 98.6 0.256 0.308 0.169 0.97 4.3 3 70169 38.7
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 2.3 2.35 99.3 2.014 2.453 1.382 0.17 0.6
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 2.3 124.091 70169 3634 98.558 0.218 0.2159 0.2201 0.2629 0.2634 42.784
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] -0.735 0.434 -1.087 1.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.62 r_dihedral_angle_6_deg 14.512 r_lrange_it 8.932 r_lrange_other 8.931 r_dihedral_angle_1_deg 8.188 r_scangle_it 6.432 r_scangle_other 6.432 r_mcangle_other 5.064 r_mcangle_it 5.061 r_scbond_it 4.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.62 r_dihedral_angle_6_deg 14.512 r_lrange_it 8.932 r_lrange_other 8.931 r_dihedral_angle_1_deg 8.188 r_scangle_it 6.432 r_scangle_other 6.432 r_mcangle_other 5.064 r_mcangle_it 5.061 r_scbond_it 4.034 r_scbond_other 4.033 r_mcbond_it 3.293 r_mcbond_other 3.293 r_dihedral_angle_2_deg 2.189 r_angle_refined_deg 0.605 r_xyhbond_nbd_refined 0.252 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_refined 0.235 r_angle_other_deg 0.227 r_symmetry_nbd_other 0.213 r_nbd_refined 0.21 r_metal_ion_refined 0.19 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.176 r_symmetry_xyhbond_nbd_other 0.106 r_ncsr_local_group_1 0.101 r_ncsr_local_group_14 0.099 r_ncsr_local_group_37 0.096 r_ncsr_local_group_2 0.094 r_ncsr_local_group_40 0.094 r_ncsr_local_group_13 0.09 r_ncsr_local_group_32 0.089 r_ncsr_local_group_27 0.088 r_ncsr_local_group_7 0.087 r_ncsr_local_group_38 0.087 r_ncsr_local_group_21 0.086 r_ncsr_local_group_39 0.085 r_ncsr_local_group_5 0.084 r_ncsr_local_group_33 0.084 r_ncsr_local_group_15 0.082 r_ncsr_local_group_34 0.082 r_ncsr_local_group_18 0.081 r_ncsr_local_group_8 0.08 r_ncsr_local_group_16 0.08 r_ncsr_local_group_20 0.08 r_ncsr_local_group_41 0.08 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_26 0.079 r_ncsr_local_group_29 0.079 r_ncsr_local_group_10 0.078 r_ncsr_local_group_9 0.077 r_ncsr_local_group_12 0.077 r_ncsr_local_group_28 0.077 r_ncsr_local_group_35 0.077 r_ncsr_local_group_22 0.076 r_ncsr_local_group_17 0.075 r_ncsr_local_group_43 0.075 r_ncsr_local_group_3 0.074 r_ncsr_local_group_4 0.074 r_ncsr_local_group_6 0.073 r_ncsr_local_group_36 0.073 r_ncsr_local_group_44 0.072 r_ncsr_local_group_45 0.07 r_ncsr_local_group_11 0.069 r_ncsr_local_group_23 0.069 r_ncsr_local_group_31 0.067 r_ncsr_local_group_42 0.067 r_ncsr_local_group_19 0.064 r_ncsr_local_group_46 0.061 r_ncsr_local_group_30 0.06 r_ncsr_local_group_24 0.057 r_ncsr_local_group_25 0.052 r_chiral_restr 0.034 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11891 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 239
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing MxCuBE data collection Coot model building