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Clostridium difficile TcdB-GTD bound to PA41 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVM 2BVM, 3L5X experimental model PDB 3L5X 2BVM, 3L5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 0.1 M Bis-Tris pH 5.5
1 M NaCl
11% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.05 59.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.13 α = 90 b = 251.74 β = 90 c = 224.45 γ = 90
Symmetry Space Group C 2 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 100 CCD RAYONIX MX-225 2015-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.79 60.85 99.9 0.161 0.996 7.5 8.5 68012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.84 99.9 1.526 0.569 6.3
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 2BVM, 3L5X 2.79 60.849 1.34 67920 2500 99.8 0.2424 0.2405 0.2468 0.2916 0.2955
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 11.243 f_angle_d 0.455 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15152 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction XSCALE data scaling PHASER phasing