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Scai scanner

Manufactured by Zeiss

The SCAI scanner is a high-performance scanning device designed for precision measurements. It utilizes advanced optical technologies to capture detailed digital representations of physical objects. The SCAI scanner's core function is to accurately digitize and analyze complex geometries, enabling detailed inspection and quality control processes.

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4 protocols using scai scanner

1

Evaporated Carbon Layer Characterization

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A deposition system (Balzers Med010) was used to evaporate a homogeneous layer of carbon. The samples were collected over 400 mesh Cu grids. The grids were then negatively stained with a solution of 1% (w/w) uranyl acetate. Micrographs were recorded on an FEI Tecnai Sphera microscope operating at 200 kV and equipped with a LaB6 electron gun, using the standard cryotransfer holders developed by Gatan, Inc. For image processing, micrographs were digitized in a Zeiss SCAI scanner with different sampling windows.
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2

Cryo-EM Imaging of MUC2 Mucin

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For MUC2D3CysD1-MG images were recorded with an FEI CM 120 electron microscope operating at an accelerating voltage of 120 kV onto Kodak SO-163 films at a magnification of 45,000 ×. The defocus values were in the range of 0.5-1.5 μm. Films were developed in concentrated Kodak D-19 developer for 12 min. To determine the quality of the micrographs, optical diffraction was used. Micrographs where digitized using a Zeiss SCAI scanner with a spacing corresponding to ~ 3.11 Å/pixel at the specimen level. For MUC2D3CysD1-M and MUC2D3 data was collected by the use of a Jeol JEM2100F field emission gun transmission electron microscope operating at 200 kV. Micrographs were recorded at a magnification of 56,600 × corresponding to ~2.67 Å/pixel on a 4K × 4K CCD camera (Tietz Video and imaging processing system). Defocus values were in the range of 1.5-2.5 μm. All images were recorded with an electron dose of 12-15 e per Å2.
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3

Electron Microscopy Analysis of Crystalline Proteins

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Images were recorded on Kodak SO-163 film with a JEOL 3000 SFF electron microscope at a nominal temperature of 4 K, an acceleration voltage of 300 kV, a magnification of x 53,000 in spot scan mode at 0.2–1 μm defocus. Crystal quality was evaluated by optical diffraction. Well-ordered areas of 4000 × 4000 or 6000 × 6000 pixels were digitized at 7 μm step size on a Zeiss SCAI scanner. Images were processed using the 2dx software (Gipson et al., 2007 (link)) and data quality was improved by synthetic unbending (Arheit et al., 2012 (link)). Projection maps were calculated from at least six lattices and were of similar quality to 6 Å resolution (Figure 4, Supplementary file 1).
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4

Vitrifying Particles for Cryo-EM Imaging

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To vitrify particles for cryo-EM observation from defined conditions of elevated temperature and humidity, we used a custom-made environmental chamber that mounts over a cryo-station (see Fig. S1 in the supplemental material). In brief, 3-μl drops of specimen were applied to EM grids mounted within the chamber, incubated for 10 min at 65°C or 70°C, and then blotted to thin films and vitrified in an otherwise conventional manner. Finally, grids were transferred into the electron microscope and low-dose micrographs were recorded on a CM200-FEG electron microscope (FEI, Hillsboro, OR) equipped with a Gatan 626 cryo-holder using procedures previously described (43 (link)). The Head I* sample was imaged at a magnification of ×38,000 and defocus values in the range of 0.78 µm to 2.15 µm. Films were digitized with a Zeiss SCAI scanner with a 7-µm sampling rate to yield 1.84 Å/pixel at the sample. The Head I sample was imaged at a magnification of ×50,000, and films were scanned on a Nikon Super CoolScan 9000 scanner with a 6.35-µm sampling rate, yielding 1.27 Å/pixel. Capsid diameters were measured by hand as averages of three measurements at positions 60° apart for each capsid. To estimate the incidence of damaged capsids, ~400 capsids from three representative micrographs were scored independently for each sample by two observers.
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