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

SASDPP4 – Consensus SAXS Profile - Ribonuclease A

Ribonuclease pancreatic
MWexperimental 14 kDa
MWexpected 14 kDa
VPorod 18 nm3
log I(s) 1.06×100 1.06×10-1 1.06×10-2 1.06×10-3
Ribonuclease pancreatic small angle scattering data  s, nm-1
ln I(s)
Ribonuclease pancreatic Guinier plot ln 1.06×100 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
Ribonuclease pancreatic Kratky plot 1.104 0 √3 sRg
p(r)
Ribonuclease pancreatic pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.9 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Ribonuclease pancreatic DAMMIN model
log I(s)
 s, nm-1
Ribonuclease pancreatic PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Ribonuclease pancreatic PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Ribonuclease pancreatic PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Ribonuclease pancreatic WAXSIS model
The consensus SAXS profile for RNaseA was generated using the datcombine tool (ATSAS 3.1.0) with both outlier- and error-filters applied. The data input to datcombine were nine scattering profiles made up of pure SEC-SAXS (5), pure batch SAXS (2) and merged SEC-SAXS-batch SAXS (2) 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 Tris, pH 7.5, 100 mM NaCl. Protein concentrations for batch measurements ranged from 1 - 18 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 ribonuclease A atomistic model for CRYSOL, Pepsi-SAXS, and FoXS calculations is the PDB ID 7RSA 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
Ribonuclease pancreatic (RNaseA)
Mol. type   Protein
Organism   Bos taurus
Olig. state   Monomer
Mon. MW   13.7 kDa
 
UniProt   P61823 (27-150)
Sequence   FASTA
 
PDB ID   7RSA
 
PDB ID   7RSA