1RD9

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529838% PEG 300, 50 mM NaCl, 100 mM Tris-HCl, and 2.3mM BV2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.983α = 90
b = 66.072β = 105.84
c = 77.818γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000ALS8.2.2

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
11.445092.40.08314.43.68630781971-316.7
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)
1.441.573.30.5671.93.16452

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.4437.5377876409092.010.133940.133940.131370.18357RANDOM12.551
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]
-0.01-0.02-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free19.22
r_scangle_it7.499
r_sphericity_bonded7.2
r_dihedral_angle_1_deg6.976
r_scbond_it5.667
r_mcangle_it4.444
r_mcbond_it3.455
r_rigid_bond_restr2.48
r_angle_refined_deg1.464
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free19.22
r_scangle_it7.499
r_sphericity_bonded7.2
r_dihedral_angle_1_deg6.976
r_scbond_it5.667
r_mcangle_it4.444
r_mcbond_it3.455
r_rigid_bond_restr2.48
r_angle_refined_deg1.464
r_angle_other_deg0.88
r_nbd_other0.335
r_symmetry_vdw_refined0.309
r_symmetry_vdw_other0.29
r_nbd_refined0.225
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.107
r_chiral_restr0.092
r_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_other0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4079
Nucleic Acid Atoms
Solvent Atoms491
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement