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) DOI

SASDPT4 – Consensus SAXS Profile - Lysozyme

Lysozyme C
MWexperimental 14 kDa
MWexpected 14 kDa
VPorod 19 nm3
log I(s) 1.05×100 1.05×10-1 1.05×10-2 1.05×10-3
Lysozyme C small angle scattering data  s, nm-1
ln I(s)
Lysozyme C Guinier plot ln 1.06×100 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
Lysozyme C Kratky plot 1.104 0 √3 sRg
p(r)
Lysozyme C pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Lysozyme C DAMMIN model
log I(s)
 s, nm-1
Lysozyme C PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Lysozyme C PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Lysozyme C PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Lysozyme C PDB (PROTEIN DATA BANK) model
The consensus SAXS profile for lysozyme was generated by the datcombine tool (ATSAS 3.1.0) with both outlier- and error-filters applied. The data input to datcombine were ten scattering profiles made up of pure SEC-SAXS (1), pure batch SAXS (4) and merged SEC-SAXS-batch SAXS (5) 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 50 mM sodium citrate, pH 4.5, 150 mM NaCl. Protein concentrations for batch measurements ranged from 0.75 - 13.4 mg/mL, and all batch data that showed evidence of aggregation or interparticle interference were merged with SEC-SAXS or lower concentration data to remove any influence from aggregate. The starting lysozyme atomistic model for CRYSOL, Pepsi-SAXS, and FoXS calculations was the PDB ID 2VB1 with small-molecule crystallisation agents removed. 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
Lysozyme C
Mol. type   Protein
Organism   Gallus gallus
Olig. state   Monomer
Mon. MW   14.3 kDa
 
UniProt   P00698 (19-147)
Sequence   FASTA
 
PDB ID   2VB1
 
PDB ID   2VB1