6HMY

Cholera toxin classical B-pentamer in complex with fucosyl-GM1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ELB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7293.150.1 M Bicine-Tris, 6% PEG1000, 6% PEG3350, 6% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.5451.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.626α = 90
b = 74.137β = 105.59
c = 111.245γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.980802MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.644.3298.40.1764.92.6150674
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.630.9640.449

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 REPLACEMENTTHROUGHOUT5ELB1.644.32143082759298.190.185170.183640.21414RANDOM13.369
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]
-0.010.230.67-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg20.872
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg13.303
r_long_range_B_refined3.862
r_long_range_B_other3.862
r_angle_refined_deg1.831
r_scangle_other1.05
r_angle_other_deg0.998
r_mcangle_it0.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg20.872
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg13.303
r_long_range_B_refined3.862
r_long_range_B_other3.862
r_angle_refined_deg1.831
r_scangle_other1.05
r_angle_other_deg0.998
r_mcangle_it0.812
r_mcangle_other0.812
r_scbond_it0.66
r_scbond_other0.66
r_mcbond_it0.481
r_mcbond_other0.48
r_chiral_restr0.083
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms8140
Nucleic Acid Atoms
Solvent Atoms797
Heterogen Atoms922

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing