☰ Navigation Tabs
Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 1 C-terminal substitution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QRE 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 8 293.15 Crystallization mix:
20% PEG6000
0.2 M lithium chloride
0.1 M Tris pH 8.0
Protein storage buffer:
0.05 M Tris/HCl pH 7.5
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.308 α = 90 b = 91.091 β = 106.403 c = 72.291 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 EIGER X 9M 2022-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 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 1.6 48.84 96.71 0.085 0.092 0.034 0.999 10.8 7.1 95507 29.3
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 1.66 92.1 2.808 3.022 1.108 0.436 0.7 7.4
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 1.603 48.84 94960 4607 96.709 0.187 0.185 0.1942 0.2215 0.2297 28.494
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] -0.734 -0.793 2.226 -0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.691 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_1_deg 7.248 r_lrange_it 5.87 r_lrange_other 5.87 r_scangle_it 4.399 r_scangle_other 4.399 r_mcangle_other 3.513 r_mcangle_it 3.507 r_scbond_it 2.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.691 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_1_deg 7.248 r_lrange_it 5.87 r_lrange_other 5.87 r_scangle_it 4.399 r_scangle_other 4.399 r_mcangle_other 3.513 r_mcangle_it 3.507 r_scbond_it 2.943 r_scbond_other 2.942 r_dihedral_angle_2_deg 2.811 r_mcbond_it 2.471 r_mcbond_other 2.462 r_angle_refined_deg 1.487 r_angle_other_deg 0.524 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.193 r_nbd_other 0.18 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.134 r_ncsr_local_group_4 0.095 r_ncsr_local_group_1 0.094 r_ncsr_local_group_3 0.089 r_metal_ion_refined 0.087 r_ncsr_local_group_2 0.087 r_symmetry_xyhbond_nbd_refined 0.085 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_8 0.074 r_symmetry_xyhbond_nbd_other 0.073 r_ncsr_local_group_10 0.07 r_ncsr_local_group_9 0.067 r_ncsr_local_group_5 0.066 r_ncsr_local_group_6 0.061 r_ncsr_local_group_7 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5885 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing Coot model building MxCuBE data collection XDS data reduction