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

SASDPV4 – Consensus SANS Profile - Lysozyme in 100% v/v D2O buffer

Lysozyme C
MWexperimental 14 kDa
MWexpected 14 kDa
log I(s) 9.43×10-1 9.43×10-2 9.43×10-3 9.43×10-4
Lysozyme C small angle scattering data  s, nm-1
ln I(s)
Lysozyme C Guinier plot ln 9.43×10-1 Rg: 1.2 nm 0 (1.2 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: 1.2 nm 0 Dmax: 3.8 nm

Data validation

Fits and models

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 OTHER model
The consensus SANS profile for lysozyme 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 sodium citrate, pH 4.5, 150 mM NaCl. Protein concentrations for batch measurements ranged from 4 - 9 mg/mL. The lysozyme atomistic model for CRYSON and Pepsi-SANS fits was the PDB ID 2VB1 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 four 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
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