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

SASDPU4 – Consensus SANS Profile - Ribonuclease A in 100% v/v D2O buffer

Ribonuclease pancreatic
MWexperimental 14 kDa
MWexpected 14 kDa
log I(s) 9.99×10-1 9.99×10-2 9.99×10-3 9.99×10-4
Ribonuclease pancreatic small angle scattering data  s, nm-1
ln I(s)
Ribonuclease pancreatic Guinier plot ln 9.99×10-1 Rg: 1.4 nm 0 (1.4 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: 1.4 nm 0 Dmax: 4.4 nm

Data validation

Fits and models

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 OTHER model
The consensus SANS profile for RNaseA in D2O buffer is a merge of a SEC-SANS data set with a consensus batch SANS data set generated using the datcombine tool (ATSAS 3.1.0) with both outlier- and error-filters applied. All contributing data were independent measurements, and no individual measurement was represented more than once in the contributing scattering profile set. The buffer was 50 mM Tris, pH 7.5, 100 mM NaCl. Protein concentrations for batch measurements ranged from 3 - 8 mg/mL. The ribonuclease A atomistic model for CRYSON and Pepsi-SANS fits was the PDB ID 7RSA with small-molecule crystallisation agents removed. Custom WAXSiS-type calculations (with neutron scattering factors and Gromacs software) used the same coordinates and added explicit waters and appropriate number of ions for the MD calculations.

The six batch data set inputs to datcombine are made available for download in the associated zip file, including also the unsubtracted 6 column format data with resolution data. Model fits are shown in order (top to bottom): CRYSON, Pepsi-SANS, and custom WAXSiS (with neutron scattering factors). The quoted pH value is the direct pH meter reading (pD uncorrected), as per modern practice.

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