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Cholera toxin classical B-pentamer in complex with Lewis-y
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 0.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding.
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.333 α = 90 b = 98.984 β = 90 c = 152.019 γ = 90
Symmetry Space Group P 21 21 21
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-F 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.08 49.5 78.9 12.48 5.7 369957
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.14 19.3 1 2.7
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 1.08 49.49 351626 18334 78.95 0.12221 0.1205 0.1206 0.15548 0.1553 RANDOM 14.551
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] 0.54 0.91 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.333 r_sphericity_free 38.855 r_dihedral_angle_4_deg 30.642 r_sphericity_bonded 12.706 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_1_deg 7.173 r_long_range_B_refined 5.915 r_long_range_B_other 5.915 r_rigid_bond_restr 3.535 r_scangle_other 3.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.333 r_sphericity_free 38.855 r_dihedral_angle_4_deg 30.642 r_sphericity_bonded 12.706 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_1_deg 7.173 r_long_range_B_refined 5.915 r_long_range_B_other 5.915 r_rigid_bond_restr 3.535 r_scangle_other 3.193 r_scbond_it 2.68 r_scbond_other 2.68 r_angle_refined_deg 2.218 r_mcangle_other 1.882 r_mcangle_it 1.881 r_mcbond_it 1.634 r_mcbond_other 1.603 r_angle_other_deg 1.295 r_chiral_restr 0.192 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8140 Nucleic Acid Atoms Solvent Atoms 1550 Heterogen Atoms 707
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing