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Crystal structure of Peptono Toxin, a diphtheria toxin homolog, from Seinonella peptonophila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 uL SPT (15.8 mg/mL in 20 mM Tris pH 8.0, 150 mM NaCl) and 1 uL mother liquor (100 mM potassium iodide, 22% PEG3350) dehydrated over 200 uL of mother liquor
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.653 α = 90 b = 82.456 β = 90 c = 91.815 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 9M 2019-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 2.0 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.185 59.291 92.7 0.118 0.124 0.047 0.996 16.4 11.5 28929 28.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.185 2.192 54 0.587 0.69 0.353 0.663 3.3
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 SAD FREE R-VALUE 2.19 59.29 1.4 28814 1462 92.66 0.2024 0.2012 0.2009 0.2243 0.2237 33.38
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 12.9158 f_angle_d 0.4885 f_chiral_restr 0.0425 f_plane_restr 0.0039 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4662 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 26
Software Software Software Name Purpose autoPROC data processing autoPROC data reduction autoPROC data scaling PHENIX phasing PHENIX refinement