| MWexperimental | 137 | kDa |
| MWexpected | 136 | kDa |
| VPorod | 220 | nm3 |
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log I(s)
1.12×100
1.12×10-1
1.12×10-2
1.12×10-3
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s, nm-1
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A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking
Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q, Hub J, Hura G, Irving T, Jeffries C, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg D, Ryan T, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss T, Whitten A, Wood K, Zuo X, Acta Crystallographica Section D Structural Biology 78(11) (2022) DOISASDPQ4 – Consensus SAXS Profile - Urate Oxidase
Uricase|
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Fits and models
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The consensus SAXS profile for urate oxidase was generated by the datcombine tool (ATSAS 3.1.0) with both outlier- and error-filters applied. The data input to datcombine were eleven scattering profiles made up of pure SEC-SAXS (6), pure batch SAXS (2) and merged SEC-SAXS-batch SAXS (3) data. All contributing data were independent measurements, and no individual measurement was represented more than once in the contributing scattering profile set. The buffer for substantial majority of the contributing data was 100 mM Tris, pH 8.0, 150 mM NaCl. Protein concentrations for batch measurements ranged from 1 - 7 mg/mL, and all batch data that showed evidence of aggregation were merged with SEC-SAXS or lower concentration data to remove any influence from aggregate. The urate oxidase atomistic model for CRYSOL, Pepsi-SAXS, and FoXS calculations was PDB ID 3L8W tetramer with small-molecule crystallisation agents removed, and a Modloop generated C-terminal sequence SLKSKL added to reflect the sequence for the protein as measured using SAXS. Custom WAXSiS calculations (with Gromacs software) used the same coordinates and added explicit waters and appropriate number of ions for the MD calculations.
The data input to datcombine are made available for download in the associated zip file. Model fits are shown in order (top to bottom): DAMMIN, CRYSOL, Pepsi-SAXS, FoXS, and custom WAXSiS. The unusually good statistics for the consensus SAXS data generally give rise to large χ-square values for the model fits.
Tags:
benchmark
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