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Cholera toxin B subunit in complex with fluorinated GM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MES/Imidazole pH 7.5, 0.03M MgCl2, 0.03M CaCl2, 16% PEG1000, 12% PEG3350 and 10% MPD
Crystal Properties Matthews coefficient Solvent content 2.15 42.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.516 α = 90 b = 132.516 β = 90 c = 113.853 γ = 90
Symmetry Space Group P 4 21 2
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 16M 2023-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033210 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 46.85 100 0.196 0.998 10.6 12.8 112970 27.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.405 0.418 0.667
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 46.85 1.33 112970 5701 99.9 0.1851 0.1832 0.1841 0.2213 0.2206 35.05
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0189 f_angle_d 0.7174 f_chiral_restr 0.0467 f_bond_d 0.0042 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8140 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 140
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing