5ELF

Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CHB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding.
Crystal Properties
Matthews coefficientSolvent content
2.2645.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.626α = 90
b = 84.72β = 90
c = 195.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5548.9299.69.25.2153547
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6498.81.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CHB1.5548.92145899766499.590.18110.179070.21956RANDOM20.241
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]
-1.252.12-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.446
r_dihedral_angle_4_deg26.31
r_dihedral_angle_3_deg12.505
r_dihedral_angle_1_deg7.154
r_long_range_B_other5.642
r_long_range_B_refined5.641
r_scangle_other3.13
r_mcangle_other2.179
r_mcangle_it2.178
r_scbond_it2.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.446
r_dihedral_angle_4_deg26.31
r_dihedral_angle_3_deg12.505
r_dihedral_angle_1_deg7.154
r_long_range_B_other5.642
r_long_range_B_refined5.641
r_scangle_other3.13
r_mcangle_other2.179
r_mcangle_it2.178
r_scbond_it2.054
r_scbond_other2.052
r_angle_refined_deg1.902
r_mcbond_it1.479
r_mcbond_other1.476
r_angle_other_deg1.231
r_chiral_restr0.153
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms8170
Nucleic Acid Atoms
Solvent Atoms1194
Heterogen Atoms554

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing