6OQ8 | pdb_00006oq8

Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH 7F


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1M Tris, pH 8.8, 0.4 M ammonium sulfate, and 24% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1661.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.711α = 90
b = 114.711β = 90
c = 301.01γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97919APS24-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
12.2107.1999.60.1119.213.4112567
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)
12.22.260.63

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.2107.1997145515799.630.198530.197360.20.219890.22RANDOM32.767
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]
0.10.1-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.469
r_dihedral_angle_4_deg20.347
r_dihedral_angle_3_deg14.388
r_dihedral_angle_1_deg5.668
r_long_range_B_refined4.86
r_mcangle_it2.141
r_scbond_it1.553
r_mcbond_it1.235
r_angle_refined_deg0.898
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.469
r_dihedral_angle_4_deg20.347
r_dihedral_angle_3_deg14.388
r_dihedral_angle_1_deg5.668
r_long_range_B_refined4.86
r_mcangle_it2.141
r_scbond_it1.553
r_mcbond_it1.235
r_angle_refined_deg0.898
r_chiral_restr0.082
r_bond_refined_d0.003
r_gen_planes_refined0.003
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 Atoms10683
Nucleic Acid Atoms
Solvent Atoms1001
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing