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

SASDPX4 – Consensus SANS Profile - Urate oxidase in 100% v/v D2O buffer

Uricase
MWexperimental 137 kDa
MWexpected 136 kDa
log I(s) 1.08×100 1.08×10-1 1.08×10-2 1.08×10-3
Uricase small angle scattering data  s, nm-1
ln I(s)
Uricase Guinier plot ln 1.08×100 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Uricase Kratky plot 1.104 0 √3 sRg
p(r)
Uricase pair distance distribution function Rg: 3.1 nm 0 Dmax: 9.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Uricase PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Uricase PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Uricase OTHER model
The consensus SANS profile for urate oxidase in D2O buffer is the consensus batch+SEC-SANS data set generated using the datcombine tool (ATSAS 3.1.0) with both outlier- and error-filters applied. One SEC-SAXS and five batch data sets were input to datcombine. All contributing data were independent measurements, and no individual measurement was represented more than once in the contributing scattering profile set. The buffer was 100 mM Tris, pH 8.0, 150 mM NaCl in D2O. Protein concentrations for batch measurements ranged from 1 – 3.6 mg/mL. The urate oxidase atomistic model for CRYSON and Pepsi-SANS fits was the PDB ID 3L8W tetramer with small-molecule crystallisation agents removed and a Modloop generated C-terminal sequence SLKSKL added. 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 data input 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
Uricase
Mol. type   Protein
Organism   Aspergillus flavus
Olig. state   Tetramer
Mon. MW   34.1 kDa
 
UniProt   Q00511 (2-302)
Sequence   FASTA
 
PDB ID   3L8W
 
PDB ID   3L8W