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Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate, 18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.87 57.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.82 α = 90 b = 169.82 β = 90 c = 79.12 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.97 147.07 99.9 12.5 8.6 14517
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.97 3.14 1.373
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6OQ5 2.97 147.07 11773 599 86.37 0.25973 0.25902 0.2591 0.27381 0.2742 RANDOM 57.304
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 -1.06 3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_4_deg 23.144 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.216 r_long_range_B_refined 0.979 r_mcangle_it 0.39 r_mcbond_it 0.216 r_scbond_it 0.188 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_4_deg 23.144 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.216 r_long_range_B_refined 0.979 r_mcangle_it 0.39 r_mcbond_it 0.216 r_scbond_it 0.188 r_chiral_restr 0.101 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 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 Atoms Number Protein Atoms 3719 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing