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Cholera toxin El Tor B-pentamer in complex with A 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, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.543 α = 90 b = 82.973 β = 90 c = 196.555 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 2014-07-06 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) R Merge I (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 1.6 49.14 99.3 0.126 6.6 4.7 136523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 98.9 1.035 0.49 4.7
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 1.6 49.14 129701 6822 99.19 0.18498 0.18281 0.1924 0.22649 0.2353 RANDOM 21.341
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] -0.13 1.32 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.706 r_dihedral_angle_4_deg 25.584 r_dihedral_angle_3_deg 13.075 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 5.41 r_long_range_B_other 5.41 r_scangle_other 3.177 r_mcangle_other 2.368 r_mcangle_it 2.366 r_scbond_it 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.706 r_dihedral_angle_4_deg 25.584 r_dihedral_angle_3_deg 13.075 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 5.41 r_long_range_B_other 5.41 r_scangle_other 3.177 r_mcangle_other 2.368 r_mcangle_it 2.366 r_scbond_it 2.044 r_scbond_other 2.042 r_angle_refined_deg 1.809 r_mcbond_it 1.552 r_mcbond_other 1.546 r_angle_other_deg 1.1 r_chiral_restr 0.168 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8170 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing