Table 2 SAXS data collection, analysis, and modelling.

From: Structure and oligomerization of the periplasmic domain of GspL from the type II secretion system of Pseudomonas aeruginosa

 

GspLperi

dimer

tetramer

 

SASBDB code

SASDDB8

SASDDC8

Data collection parameters

 

Beamline

SWING, Soleil, Paris

 

Detector

PCCD170170 (AVIEX)

 

Beam geometry, mm2

1 × 0.5

 

Wavelength, Ã…

1.03

 

Mode

SEC

 

Column

4.6 × 300 mm Bio SEC-3

 

Initial concentration, mg/ml

13.7

9.0

 

Injected volume, µl

50

 

Flow rate, ml/min

0.2

 

Temperature, °C

15

Software employed

 

Primary data reduction

FOXTROT

 

Data processing

Primus, Gnom55,56

 

Ab initio analysis

DAMMIF36

 

validation and averaging

DAMAVER57

 

Modelling

EOM38

 

Computation of model intensities

Crysol55

 

3D graphics representation

Pymol

Structural parameters

Guinier Analysis

 

I(0)

0.037 ± 2.5e-5

0.039 ± 2.3e-5

 

Rg, Ã…

22.42 ± 0.03

31.75 ± 0.37

 

Qmin, 1/Ã…

0,0018

0,0025

 

qRgmax

1.23

1.23

 

M from I(0), (ratio to predicted value)

1.30

1.05

P(r) analysis

 

I(0)

0.039 ± 0.91e-5

0.037 ± 0.27e-4

 

Rg, Ã…

22.43 ± 0.07

30.98 ± 0.03

 

Dmax, Ã…

75

105

 

q range, 1/Ã…

0.0018–0.517

0.0025–0.517

 

M from I(0), (ratio to predicted value)

1.37

1.00

 

Porod volume estimate, Ã…3 (ratio V/calc. MW)

30128 (1.08)

60526 (1.08)

 

dry volume from sequence, Ã…3

33777

67554

Molecular mass determination

 

SAXS_MoW server, kDa

22.8

83

 

Scatter software, kDa

32.7

63.9

 

calculated from sequence, kDa

27.9

55.8

 

determined by MALS, kDa

27.5

55.5

Shape model-fitting results

DAMMIF (default parameters, 20 models)

 

q range for fitting, 1/Ã…

0.0018–0.517

0.0025–0.517

 

Symmetry and anisotropy assumptions

P1, none

P1, none

 

NSD (standard deviation), no. of clusters

1.036 (0.0022), 3

1.065 (0.0038), 4

 

χ2 range

2.474–2.528

2.826–2.875

 

Constant adjustment to intenities

Skipped, unable to detrmine

 

MW estimate (ratio to predicted value)

15.2 (0.54)

31.95 (0.57)

EOM (default parameters, 10 000 models in initial ensemble, native-like models)

 

χ2

5.788

NA

 

number of representative structures

6

NA