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Clostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with apigenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.1 M HEPES pH 7.5-8.5, 0.2 M Mg(CH3CHOO)2, PEG 3350 5-25%
Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.09 α = 90 b = 154.81 β = 90 c = 271.36 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-300 2016-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.75 44.437 99.75 0.549 21.33 6.6 45388
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 2.75 44.437 1.33 45276 1978 99.78 0.1981 0.1964 0.2015 0.2359 0.2405
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 21.595 f_angle_d 0.906 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8820 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing