5ELB

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding.
Crystal Properties
Matthews coefficientSolvent content
2.3447.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.333α = 90
b = 98.984β = 90
c = 152.019γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

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
11.0849.578.912.485.7369957
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.081.1419.312.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CHB1.0849.493516261833478.950.122210.12050.140.155480.17RANDOM14.551
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]
0.540.91-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.333
r_sphericity_free38.855
r_dihedral_angle_4_deg30.642
r_sphericity_bonded12.706
r_dihedral_angle_3_deg11.614
r_dihedral_angle_1_deg7.173
r_long_range_B_refined5.915
r_long_range_B_other5.915
r_rigid_bond_restr3.535
r_scangle_other3.193
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8140
Nucleic Acid Atoms
Solvent Atoms1550
Heterogen Atoms707

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing