Small-Angle X-ray Scattering data (benchmarking/consensus): EMBL-P12 SAXS beam line, DESY

Clement Blanchet, Melissa Graewert, Cy M Jeffries, Dmitri Svergun.

SASDPK7 – Xylose isomerase SEC-SAXS data (EMBL-P12 bioSAXS beam line at DESY)

Xylose isomerase
MWexperimental 167 kDa
MWexpected 173 kDa
VPorod 228 nm3
log I(s) 1.79×10-1 1.79×10-2 1.79×10-3 1.79×10-4
Xylose isomerase small angle scattering data  s, nm-1
ln I(s)
Xylose isomerase Guinier plot ln 1.80×10-1 Rg: 3.2 nm 0 (3.2 nm)-2 s2
Xylose isomerase Kratky plot 1.104 0 3 sRg
Xylose isomerase pair distance distribution function Rg: 3.2 nm 0 Dmax: 14.1 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of Xylose isomerase (a.k.a. glucose isomerase) in 50 mM Tris, 100 mM NaCl, 1 mM MgCl2, 1 % v/v glycerol, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 75.00 μl sample at 11 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 27 successive 1 second frames were collected through the main SEC elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The quoted experimental MW was determined from MALLS/RI data. The full entry .zip archive contains MW estimates from MALLS/UV and from I(0) and concentration in addition to the relative- and absolute-scaled unsubtracted SEC-SAXS data frames collected through the entire SEC-elution (2400 data frames), the CHROMIXS Rg-correlation through the SEC-elution peak, and the selected unsubtracted sample and buffer frames used to generate the profile displayed in this entry. Repulsive interparticle interference is present in the sample. These data form part of the 'Consensus and benchmarking SAS data project' by Trewhella et al., 2022:

Tags: benchmark
Xylose isomerase
Mol. type   Protein
Organism   Streptomyces rubiginosus
Olig. state   Tetramer
Mon. MW   43.2 kDa
UniProt   P24300 (1-388)
Sequence   FASTA