6OQ6

Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6OQ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M Tris, pH 8.5, 0.2 M lithium sulfate, 18% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.8757.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.82α = 90
b = 169.82β = 90
c = 79.12γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97920APS24-ID-C

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
12.97147.0799.912.58.614517
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)
12.973.141.373

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6OQ52.97147.071177359986.370.259730.259020.27381RANDOM57.304
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]
-1.06-0.53-1.063.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.645
r_dihedral_angle_4_deg23.144
r_dihedral_angle_3_deg21.266
r_dihedral_angle_1_deg6.556
r_angle_refined_deg1.216
r_long_range_B_refined0.979
r_mcangle_it0.39
r_mcbond_it0.216
r_scbond_it0.188
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.645
r_dihedral_angle_4_deg23.144
r_dihedral_angle_3_deg21.266
r_dihedral_angle_1_deg6.556
r_angle_refined_deg1.216
r_long_range_B_refined0.979
r_mcangle_it0.39
r_mcbond_it0.216
r_scbond_it0.188
r_chiral_restr0.101
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 Atoms3719
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing