5ELD

Cholera toxin classical B-pentamer in complex with A Lewis-y


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.72930.1 M MES-Imidazole, 25% PEG4000, 5% PGA-LM
Crystal Properties
Matthews coefficientSolvent content
2.8256.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.7α = 90
b = 69.806β = 90
c = 134.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.448.599.10.07610.854.3129054
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4898.10.9931.264.2

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 REPLACEMENTTHROUGHOUT3CHB1.448.48122617643899.070.172260.171110.19347RANDOM17.125
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]
-0.650.310.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.056
r_dihedral_angle_4_deg27.755
r_dihedral_angle_3_deg12.75
r_dihedral_angle_1_deg6.848
r_long_range_B_refined5.253
r_long_range_B_other5.253
r_scangle_other2.836
r_mcangle_other2.204
r_mcangle_it2.202
r_angle_refined_deg1.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.056
r_dihedral_angle_4_deg27.755
r_dihedral_angle_3_deg12.75
r_dihedral_angle_1_deg6.848
r_long_range_B_refined5.253
r_long_range_B_other5.253
r_scangle_other2.836
r_mcangle_other2.204
r_mcangle_it2.202
r_angle_refined_deg1.806
r_scbond_it1.801
r_scbond_other1.801
r_mcbond_it1.382
r_mcbond_other1.379
r_angle_other_deg1.335
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.005
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 Atoms4070
Nucleic Acid Atoms
Solvent Atoms610
Heterogen Atoms333

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing