6OQ5 | pdb_00006oq5

Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVL2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 4R042BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 3PEE2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 6C0B2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 3V0A2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 4NP42BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental modelPDB 4NC22BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M sodium acetate, 0.1M magnesium acetate, and 5% PEG 8K (final pH 5.2)
Crystal Properties
Matthews coefficientSolvent content
3.5865.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.619α = 90
b = 168.565β = 90
c = 179.921γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152016-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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
13.8748.9199.40.1377.73.742971
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)
13.873.971.548

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 REPLACEMENTTHROUGHOUT2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC23.8748.9140731220399.220.265410.262750.260.315160.32RANDOM169.399
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]
-2.62.480.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.591
r_long_range_B_refined21.701
r_dihedral_angle_4_deg16.699
r_dihedral_angle_3_deg15.806
r_mcangle_it10.572
r_dihedral_angle_1_deg7.891
r_mcbond_it6.114
r_scbond_it5.715
r_angle_refined_deg1.097
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.591
r_long_range_B_refined21.701
r_dihedral_angle_4_deg16.699
r_dihedral_angle_3_deg15.806
r_mcangle_it10.572
r_dihedral_angle_1_deg7.891
r_mcbond_it6.114
r_scbond_it5.715
r_angle_refined_deg1.097
r_chiral_restr0.093
r_gen_planes_refined0.005
r_bond_refined_d0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21501
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing