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

SASDPW4 – Consensus SANS Profile - Xylanase in 100% v/v D2O buffer

Endo-1,4-beta-xylanase
MWexperimental 21 kDa
MWexpected 21 kDa
log I(s) 9.73×10-1 9.73×10-2 9.73×10-3 9.73×10-4
Endo-1,4-beta-xylanase small angle scattering data  s, nm-1
ln I(s)
Endo-1,4-beta-xylanase Guinier plot ln 9.74×10-1 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
Endo-1,4-beta-xylanase Kratky plot 1.104 0 √3 sRg
p(r)
Endo-1,4-beta-xylanase pair distance distribution function Rg: 1.4 nm 0 Dmax: 4.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Endo-1,4-beta-xylanase PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Endo-1,4-beta-xylanase PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Endo-1,4-beta-xylanase OTHER model
The consensus SANS profile for xylanase 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 - 11 mg/mL. The xylanase atomistic model for CRYSON and Pepsi-SANS fits was the PDB ID 2DFC 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 eight 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
Endo-1,4-beta-xylanase
Mol. type   Protein
Organism   Trichoderma longibrachiatum
Olig. state   Monomer
Mon. MW   20.8 kDa
 
UniProt   F8W669 (1-190)
Sequence   FASTA
 
PDB ID   2DFC
 
PDB ID   2DFC