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Crystal Structure of Trypsinized Clostridium perfringens Enterotoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292.15 100 mM potassium phosphate monobasic, 100 mM MES monohydrate pH 6.5, and 2.0 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 4.19 70.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.33 α = 90 b = 200.33 β = 90 c = 254.78 γ = 90
Symmetry Space Group P 43 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 EIGER X 16M 2021-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033167 APS 23-ID-B
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 2.32 66.78 99.62 0.997 7.17 14.09 222147 76.22
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 2.32 2.403 0.118 0.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.32 66.777 1.33 221336 1994 99.63 0.2241 0.2239 0.2299 0.2477 0.2513
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 11.091 f_angle_d 0.553 f_chiral_restr 0.043 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17805 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 674
Software Software Software Name Purpose PHENIX refinement XDS data reduction pointless data scaling MoRDa phasing PHASER phasing