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55 protocols using nanostar

1

SAXS Data Collection and Analysis

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SAXS data was collected at the National Magnetic Resonance Facility at Madison (NMRFAM) using a Bruker Nanostar. The Bruker Nanostar had a wavelength of 1.54 Å with a sample-detector distance set to 67.7 cm resulting in a momentum transfer range of 0.01 < q < 0.40 Å−1. Data for SAXS buffer and protein were collected at 25°C for 2–4 hours. To account for excluded volume of the protein, buffer was subtracted. For optimal data, merged data sets were generated from two different concentrations using the lowest angles from one dataset and the highest angles from another. An overlapping region of at least 60 points was utilized for the merging process. This was conducted in accordance with the Primus analysis guide. Guinier analysis was conducted to determine the Rg value through the use of the Primus software (ATSAS) [31 (link),39 (link)]. A comparison of concentrations was conducted to detect overall quality of data.
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2

SAXS Characterization of A3_bGFPD Protein

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SEC-SAXS data were collected with A3_bGFPD samples at the BM29 line at the ESRF, Grenoble, with a size-exclusion HPLC column (Agilent Bio sec-3) online with a SAXS measuring cell (a 1.5 mm diameter quartz capillary in an evacuated sample chamber) and the data analysis is detailed in Note S1.
Other SAXS experiments were performed on an in-house SAXS instrument (Brüker Nanostar; λ = 1.54 Å). 30 µl of concentrated solutions (0.5 mg mL−1 ≤ c ≤ 8.0 mg mL−1) of A3_bGFPD were placed in a quartz capillary thermalized cell inserted into an evacuated sample chamber. SAXS data were analyzed using the program PRIMUS (https://www.embl-hamburg.de/biosaxs/primus.html).
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3

WAXS Analysis of Fish Bone IBs

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Eight IBs (“small fish”: n = 3, “large fish”: n = 5) were investigated using laboratory WAXS (NanoSTAR, Bruker AXS, USA) with a CuKα X-ray source (λ: 0.154 nm, beam size: ~1 mm, acquisition time: 6 h). 2D WAXS patterns were processed using the Scherrer equation (1) with a shape factor of K = 0.9, L (crystal length), λ (X-ray wavelength), B (full width at half maximum in radians), and Ɵ (half of the respective diffraction angle) according to established protocols (Pabisch et al., 2013 (link); Turunen et al., 2016 (link)).
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4

Analyzing Lamellar Structure of Materials

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Samples were mixed with deionized water to achieve ~60% of total moisture content and equilibrated at ambient temperature (~25 °C) for 24 h. A small-angle X-ray scattering diffractometer (NanoSTAR, Bruker AXS Inc., Madison, WI, USA), equipped with a Vantec 2000 detector (Bruker, Berlin, Germany) and pinhole collimation for point focus geometry, were used for sample lamellar structure analysis, as described elsewhere [19 (link)]. The average repeat distance (i.e., thickness of the semicrystalline lamellae) of the amorphous and crystalline lamellar of each sample was calculated as d = 2π/q, where d (nm) is the lamellar repeat distance and q (nm−1) is the scattering vector, with q = (4π sinθ)/λ, where λ (nm) is the X-ray wavelength and 2θ is the scattering angle.
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5

3D-Printed Starch Nanostructure Analysis

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Each
3D-printed starch sample was dispersed into distilled water to form
a slurry (40% w/w) and slightly stirred with 56 s–1 (367 G-force) at ambient conditions overnight. Next, it was centrifuged
(Eppendorf centrifuge 5417R, Hamburg, Germany) at 5000 G-force for
5 min, and the wet precipitate was collected. A Bruker small-angle
X-ray scattering (SAXS) instrument (NanoSTAR, Bruker AXS Inc., Billerica,
MA) was used to record the two-dimensional (2D) scattering pattern
of printed starches at 50 kV and a 30 W Cu Kα radiation wavelength
of 1.5418 Å. The SAXS instrument was equipped with a Vantec 2000
detector and pinhole collimation for point focus geometry. The one-dimensional
(1D) scattering curves were obtained in the range of 0.2 < q < 1.4 nm–1 from the 2D scattering
patterns through the built-in software. The SAXS curves were further
analyzed with the help of the 1D linear correlation function L(r) (eq 3) Here, q is the scattering
vector, I(q) is the scattering intensity, r is the distance in real space, and the denominator is
the scattering invariant.
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6

SAXS Characterization of Liquid Samples

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For the SAXS experiment, liquid samples (each 80 μL) were loaded into a standard Bruker quartz liquid holder. For each sample, the scattering and transmittance were measured separately. SAXS measurements were conducted on a Bruker NanoSTAR instrument. X-rays were generated by a Turbo (rotating anode) X-ray source (TXS). A wavelength of 1.542 Å was chosen from the Cu-Kα emission using a Göbel mirror. A pair of “scatterless” pinholes with diameters of 500 and 350 μm were used for beam collimation. The 2-D intensity data was collected by a MikroGap VÅNTEC-2000 detector with a sample-to-detector distance of 108 cm to cover a scattering vector q ranging from 0.007 to 0.25 Å–1. The raw SAXS data was corrected for the sample transmission and the empty-cell scattering. The 1-D data (I vs. q) was obtained by circularly averaging the 2-D data with respect to the beam center.
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7

SAXS Analysis of H-GbpA-FL and D-GbpA-FL Proteins

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SAXS data were acquired
on a Bruker NanoStar instrument using 40.0 μM H-GbpA-FL or 32.0
μM D-GbpA-FL in 100 mM NaCl, 20 mM Tris–HCl pH 8.0, with
data acquisition times of 1 h per data set. Scattering intensities
were recorded as a function of the scattering vector q = (4π/λ)sinθ, where 2θ is the scattering
angle and λ is the wavelength (λ = 1.54 Å). Data
were collected in the q-range: 0.009 to 0.3 Å–1.
The scattering intensities were corrected
for electronic noise, empty cell scattering, and detector sensitivity.
The scattering contribution from the buffer was subtracted, and intensities
were calibrated to absolute units with H2O scattering as
standard, using the SUPERSAXS program package (CLP
Oliveira and JS Pedersen, unpublished; implementation explained in
ref (25 (link))).
Radii
of gyration and pair-distance distribution functions (from
inverse Fourier transform26 (link)) were calculated
with PRIMUS(27 (link)) from the ATSAS(28 (link)) package. For both H-GbpA-FL
and D-GbpA-FL, 20 low-resolution models were calculated by ab initio shape determination using the DAMMIF(29 (link)) software. We built average models with DAMAVER(30 (link)) and refined them with DAMMIN.(31 (link)) All three programs
are from the ATSAS(28 (link)) package.
SAXS data are summarized in Table 2.
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8

SAXS Structural Analysis of TM7 and TM10

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Unless noted otherwise, SAXS experiments were performed at ALS beamline 12.3.1 LBNL Berkeley, California, USA 51 (link), with a detector distance of 2 meter and X-ray wavelength of λ=1.27 Å, covering a Q range of 0.009 Å−1 to 0.4 Å−11. The data set was calibrated to an absolute intensity scale using water as a primary standard. All experiments were performed at 20°C and data were processed as previously described 52 (link).
TM7 and TM10 were measured using a Bruker NANOSTAR equipped with a microfocus X-ray source (IμS Cu, Incoatec, Germany) and a VÅNTEC-2000 detector. Raw scattering data was calibrated to absolute intensity scale using water as a primary standard and radially averaged in order to obtain the 1D scattered intensity profile as a function of the scattering vector, with a wavelength of 1.54 Å. The modelling fit analysis of the scattering data is explained in detail in subsection 1.2 of the Supplemental Information.
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9

SAXS Experiments with NANOSTAR

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The SAXS experiments were performed using the NANOSTAR, Bruker installed at ANSTO. The obtained SAXS intensity was corrected for background, empty cell, buffer solution scattering, and transmittance.
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10

Characterizing Bulk BCP Morphologies

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The bulk samples were prepared from chloroform solution. After evaporating the solvent, the samples were annealed under vacuum at each temperature. The bulk morphologies of the BCPs were characterized by small-angle X-ray scattering (SAXS). The SAXS measurement was performed using a Bruker NanoSTAR with a 2D-PSPC detector.
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