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Crystal structure of Clostridioides difficile binary toxin CDTb D4 fragment in complex with BINTOXB/9 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UWT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 10.1% PEG3350, 13.4% 2-propanol, 0.2 M ammonium citrate pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.209 α = 90 b = 111.76 β = 90 c = 148.349 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2020-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.6 55.88 99.2 0.99 8.2 5.7 50515 58.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 0.61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6UWT 2.6 55.88 1.34 50515 2482 99.21 0.2281 0.2265 0.227 0.2603 0.2592 64.54
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.6159 f_angle_d 0.5812 f_chiral_restr 0.0425 f_plane_restr 0.005 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8644 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing