1RF2

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529816% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.244.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.235α = 90
b = 66.028β = 105.8
c = 78.642γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9626ALS8.2.2

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
11.355094.20.08113.53.5111363104314-313.4
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)
1.351.469.30.5911.82.77606

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3CHB1.3549.39104314104314521993.890.134390.134390.132320.17389RANDOM10.455
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]
0.040.03-0.060.04
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.151
r_scangle_it7.194
r_dihedral_angle_1_deg6.954
r_sphericity_bonded6.669
r_scbond_it5.237
r_mcangle_it3.398
r_mcbond_it2.485
r_rigid_bond_restr2.121
r_angle_refined_deg1.417
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.151
r_scangle_it7.194
r_dihedral_angle_1_deg6.954
r_sphericity_bonded6.669
r_scbond_it5.237
r_mcangle_it3.398
r_mcbond_it2.485
r_rigid_bond_restr2.121
r_angle_refined_deg1.417
r_angle_other_deg0.862
r_symmetry_vdw_other0.348
r_nbd_other0.298
r_symmetry_hbond_refined0.265
r_symmetry_vdw_refined0.23
r_nbd_refined0.22
r_xyhbond_nbd_refined0.16
r_chiral_restr0.086
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4074
Nucleic Acid Atoms
Solvent Atoms498
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement