6OQ7 | pdb_00006oq7

Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2 M potassium acetate and 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.550.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.018α = 90
b = 104.096β = 90
c = 113.825γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.3943.1499.70.1414.67.131676
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)
12.392.450.5

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-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6OQ52.3943.1430060156299.110.199160.197150.23621RANDOM50.323
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]
3.341.44-4.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg18.394
r_dihedral_angle_3_deg17.719
r_long_range_B_refined6.357
r_dihedral_angle_1_deg6.159
r_mcangle_it3.433
r_scbond_it2.915
r_mcbond_it2.163
r_angle_refined_deg0.998
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg18.394
r_dihedral_angle_3_deg17.719
r_long_range_B_refined6.357
r_dihedral_angle_1_deg6.159
r_mcangle_it3.433
r_scbond_it2.915
r_mcbond_it2.163
r_angle_refined_deg0.998
r_chiral_restr0.081
r_gen_planes_refined0.004
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 Atoms5229
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms39

Software

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