1RDP

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529812% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.244.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.09α = 90
b = 66.079β = 105.83
c = 78.715γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9791ALS8.2.2

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
11.355091.30.05919.53.66105335100384-312.9
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)
1.351.463.80.4512.43.226952

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 3CHB1.3548.22100384100384502991.220.131940.131940.129860.17052RANDOM10.928
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]
-0.06-0.030.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.699
r_dihedral_angle_1_deg6.952
r_scangle_it6.083
r_sphericity_bonded6.002
r_scbond_it4.376
r_mcangle_it3.476
r_mcbond_it2.658
r_rigid_bond_restr2.112
r_angle_refined_deg1.501
r_angle_other_deg0.867
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.699
r_dihedral_angle_1_deg6.952
r_scangle_it6.083
r_sphericity_bonded6.002
r_scbond_it4.376
r_mcangle_it3.476
r_mcbond_it2.658
r_rigid_bond_restr2.112
r_angle_refined_deg1.501
r_angle_other_deg0.867
r_symmetry_vdw_other0.355
r_nbd_other0.297
r_symmetry_vdw_refined0.258
r_nbd_refined0.227
r_xyhbond_nbd_refined0.176
r_symmetry_hbond_refined0.146
r_chiral_restr0.088
r_nbtor_other0.085
r_bond_refined_d0.013
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 Atoms4093
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement