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Scabin (S117A) toxin from Streptomyces scabies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAZ PDB entry 5DAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 100 mM potassium chloride, 50 mM sodium cacodylate trihydrate, pH 6.0, 16% PEG1000, 0.5 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.45 α = 90 b = 60.85 β = 99.6 c = 37.95 γ = 90
Symmetry Space Group C 1 2 1
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 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979 CLSI 08ID-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 1.55 43.61 99.71 0.04171 0.04781 0.02314 0.999 17.72 4.2 28826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.605 99.62 0.9209 0.5157 0.692 1.64 4.1
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 THROUGHOUT PDB entry 5DAZ 1.55 43.606 1.35 28791 1441 99.69 0.1801 0.1786 0.1795 0.2101 0.2072 33.4009
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1284 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing