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K2 summit

Manufactured by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom

The K2 Summit is a compact and versatile laboratory equipment designed for a wide range of applications. It features a high-resolution touch screen display, a robust and durable construction, and intuitive software for easy operation. The core function of the K2 Summit is to provide precise and reliable data analysis and processing capabilities in a laboratory setting.

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33 protocols using k2 summit

1

Cryo-EM Sample Preparation Technique

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Cryo-EM samples were made by Vitrobot (FEI Company) at a controlled temperature (25 °C) and at saturation. Cryo-EM grids were frozen using a Vitrobot Mark IV (FEI) as follows: 6 μL of the sample was applied to a glow discharged Quantifoil R1.2/1.3 holey carbon 300 mesh gold grid. To remove excess solution and produce a thin liquid film the drop is blotted manually in the Vitrobot. The blotted sample is then plunged into liquid ethane (−183 °C) to form a vitrified specimen and transferred to liquid nitrogen (−196 °C) for storage. Cryo-EM data of vitrified specimens were recorded on a Titan Krios (FEI) operated at 300 kV, equipped with a Gatan K2 Summit camera. SerialEM was used for automated data collection.
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2

Cryo-EM Tilt Pair Validation of PikAIII

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The 3D cryo-EM reconstructions of PikAIII were also validated by a tilt
pair parameter test61 (link). For
tilt pair validation we recorded image pairs of PikAIII/ΔACP5with a tilt angle differential of 30°
(+15°/−15°) using a Gatan K2 Summit on a Tecnai
F20 transmission electron microscope (FEI) equipped with a field emission gun
operated at 200kV. Images were recorded at a nominal magnification of 38,673x,
corresponding to a pixel size of 1.23 Å at the specimen level. The total
dose of the first and second image was 22 e/Å2 and 28
e/Å2, respectively, and fractionated over 20 sub-frames
acquired over 4-second exposures. The sub-frames of each exposure were aligned
with the UCSF alignment program59 (link) (kindly provided by Yifan Cheng and Xueming Li) and merged.
Tilt pair validation was processed with the corresponding routines of EMAN 2.07.
102 particle projection pairs were interactively selected using
e2RCTboxer.py62 (link), and CTF corrected using e2ctf.py. The
tilt validation parameter plot (Extended Data Fig.
2c
) was obtained with the program
e2tiltvalidate.py62 (link) and shows that the majority of tilt projections pairs
cluster at the expected 30° tilt angle differential, thereby validating
the 3D map.
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3

Cryo-EM Imaging of Human PANX1 Protein

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The cryo-EM grids were prepared using Vitrobot Mark IV (FEI) operated at 4 °C and 100% humidity. For samples of hPANX1 in digitonin, 4 μl aliquots of samples at concentrations of approximately 8 mg/ml were applied onto glow-discharged holey carbon grids (Quantifoil R1.2/1.3) 300 mesh Au grid. After a waiting time of 5 s, the grids were blotted for 2 s and plunged into liquid ethane for quick freezing.
The cryo-EM grids were screened on a Tecnai Arctica microscope (FEI) operated at 200 kV using a Falcon II 4k × 4k camera (FEI). The qualified grids were transferred into a Titan Krios microscope (FEI) operated at 300 kV for data acquisition equipped with Gatan K2 Summit detector and GIF Quantum energy filter. Images were automatically recorded using AutoEMation with a slit width of 20 eV on the energy filter and in the super-resolution mode at a nominal magnification of 130,000×, corresponding to a calibrated pixel size of 1.08 Å at the object scale, and with defocus ranging from 1.4 to 1.9 μm. Each stack was exposed for 5.6 s with an exposing time of 0.175 s per frame, resulting in a total of 32 frames per stack, and the total dose rate for each stack was about 50 e/Å2.
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4

Cryo-EM Imaging of Tau Filaments

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Before making cryo-grids, the heparin-induced assembly reactions were centrifuged at 100,000 g for 30 min at 4°C. The resulting pellets were resuspended in 20 mM Tris, pH 7.4, 100 mM NaCl. Pronase-treated tau filaments (3 μl, at 2.0 mg/ml) were applied to glow-discharged holey carbon grids (Quantifoil Au R1.2/1.3, 300 mesh), blotted with filter paper and plunge-frozen in liquid ethane using an FEI Vitrobot Mark IV. For 2N4R filaments, imaging was performed on an FEI Tecnai G2 Polara microscope operating at 300 kV using a Falcon III detector prototype in integrating mode. A total of 717 movies of 30 frames was recorded during 1.0 s exposures, at a pixel size of 1.38 Å on the specimen, and a total dose of approximately 48 e/Å2. Defocus values ranged from −1.7 to −2.8 μm. For 2N3R filaments, imaging was performed on a Gatan K2-Summit detector in counting mode, using an FEI Titan Krios at 300 kV. A GIF-quantum energy filter (Gatan) was used with a slit width of 20 eV to remove inelastically scattered electrons. A total of 2051 movies of 44 frames was recorded during 11 s exposures, at a pixel size of 1.04 Å on the specimen, and a total dose of 50 electrons per Å2. Defocus values ranged from −0.8 to −2.2 μm. Further details are presented in Table 1.
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5

Cryo-EM Tomography of Microbial Specimens

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Frozen-hydrated specimens were imaged at −170 °C using a Polara G2 electron microscope (FEI Company) equipped with a field emission gun and a direct detection device (Gatan K2 Summit). The microscope was operated at 300 kV with a magnification of ×9,400, resulting in an effective pixel size of 4.5 Å at the specimen level. We used SerialEM (38 (link)) to collect low-dose, single-axis tilt series with dose fractionation mode at about 8 µm defocus. Tilt series were collected from −51° to 51° with an increment of 3° and a cumulative dose of ∼70 e2 distributed over 35 stacks. Each stack contains approximately eight images. We used Tomoauto (39 ) to facilitate data processing, which includes drift correction of dose-fractionated data using Motioncorr (40 (link)) and assembly of corrected sums into tilt series, automatic fiducial seed model generation, alignment, and contrast transfer function correction of tilt series by IMOD (41 (link)) and weighted back projection (WBP) reconstruction of tilt series into tomograms using Tomo3D (42 (link)). Each tomographic reconstruction is 3,710 × 3,838 × 1,600 pixels and ∼1.30 Gb in size. In total, 4,227 tomographic reconstructions from six different strains were generated.
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6

Cryo-EM Tilt Pair Validation of PikAIII

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The 3D cryo-EM reconstructions of PikAIII were also validated by a tilt
pair parameter test61 (link). For
tilt pair validation we recorded image pairs of PikAIII/ΔACP5with a tilt angle differential of 30°
(+15°/−15°) using a Gatan K2 Summit on a Tecnai
F20 transmission electron microscope (FEI) equipped with a field emission gun
operated at 200kV. Images were recorded at a nominal magnification of 38,673x,
corresponding to a pixel size of 1.23 Å at the specimen level. The total
dose of the first and second image was 22 e/Å2 and 28
e/Å2, respectively, and fractionated over 20 sub-frames
acquired over 4-second exposures. The sub-frames of each exposure were aligned
with the UCSF alignment program59 (link) (kindly provided by Yifan Cheng and Xueming Li) and merged.
Tilt pair validation was processed with the corresponding routines of EMAN 2.07.
102 particle projection pairs were interactively selected using
e2RCTboxer.py62 (link), and CTF corrected using e2ctf.py. The
tilt validation parameter plot (Extended Data Fig.
2c
) was obtained with the program
e2tiltvalidate.py62 (link) and shows that the majority of tilt projections pairs
cluster at the expected 30° tilt angle differential, thereby validating
the 3D map.
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7

Automated Cryo-EM and Negative Stain Imaging

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All negative stain and cryoEM data were acquired using the Leginon automated data acquisition system 26 (link). Data acquisition for negative stained samples was performed on a Tecnai Spirit (FEI) transmission electron microscope operating at 120keV. Images were collected at a nominal magnification of 52,000X on an F416 CMOS 4Kx4K camera (TVIPS) with a pixel size of 2.05 Å/pixel at specimen level. All micrographs were collected using an electron dose of 20 electrons/Å2 with a defocus range from 0.3 μm to 1.5 μm.
CryoEM data for dynactin were collected on Titan Krios (FEI) transmission electron microscope operating at 300keV, using a Gatan K2 Summit camera operated in counting mode at dose rate of ~10 electrons/pixel/s. Each movie comprised of 30 frames acquired over 6s, with a cumulative does of ~35 electrons/Å2. Imaging was performed at a nominal magnification of 22,500X, with a pixel size of 1.31 Å/pixel at specimen level using a defocus ranging from 0.8μm to 4μm.
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8

Cryo-EM Imaging of PvHK Protein

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PvHK at a concentration of 5 mg ml−1 in buffer [20 mM Tris pH 7.5, 50 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine (TCEP)] was applied to Quantifoil Cu 200 mesh grids (1.2/1.3) that were plasma cleaned using a Solarus plasma cleaner (Gatan). The sample was blotted for 3 s and plunge-frozen in liquid ethane cooled by liquid nitrogen using an FEI Vitrobot plunge-freezing instrument. The blotting chamber was maintained at 20°C and a humidity of 100%. Cryo-EM imaging was carried out with an FEI Titan Krios operating at 300 kV. Images were acquired with a K2 Summit camera placed at the end of a Gatan Imaging Filter (GIF) in super-resolution mode with a magnified pixel size of 0.4177 Å. Images were collected spanning a defocus range of 0.5–3 µm. The dose rate was ∼1.8 e per pixel per second and the exposure time was 23.2 s. Movies were collected at a rate of 2.5 frames per second, giving 58 frames per image.
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9

Cryo-EM Sample Preparation and Imaging

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For grids preparation, 3 μL concentrated protein was loaded onto glow-discharged R1.2/1.3 Quantifoil grids at 4 °C under 100% humidity. Grids were blotted for 4.5 s and plunge-frozen in liquid ethane using a Vitrobot Mark IV (FEI). Micrographs were acquired on a Titan Krios microscope (FEI) operating at a voltage of 300 kV. During one collection session (KCNQ2-CaMHN37, Supplementary Fig. 6) micrographs were collected at a magnification of 49,310× (calibrated pixel size 1.014 Å, defocus range −1.1 μm to −1.3  μm, 40 frames, and a total dose 64 e2) using a Gatan K2 Summit direct electron detection camera via SerialEM48 (link) following standard procedure. After the microscope was upgraded with a Gatan Falcon 4 camera equipped with energy filter (Thermo Fisher Scientific) with slit width set to 10 eV, additional collection sessions (Supplementary Figs. 1, 2, 8, 9) were conducted at a magnification of 130,000× (calibrated pixel size 0.93 Å, defocus range −0.8 μm to −1.5 μm, 40 frames, and a total dose 52 e2) using EPU software (Thermo Fisher Scientific).
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10

Automated Cryo-EM and Negative Stain Imaging

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All negative stain and cryoEM data were acquired using the Leginon automated data acquisition system 26 (link). Data acquisition for negative stained samples was performed on a Tecnai Spirit (FEI) transmission electron microscope operating at 120keV. Images were collected at a nominal magnification of 52,000X on an F416 CMOS 4Kx4K camera (TVIPS) with a pixel size of 2.05 Å/pixel at specimen level. All micrographs were collected using an electron dose of 20 electrons/Å2 with a defocus range from 0.3 μm to 1.5 μm.
CryoEM data for dynactin were collected on Titan Krios (FEI) transmission electron microscope operating at 300keV, using a Gatan K2 Summit camera operated in counting mode at dose rate of ~10 electrons/pixel/s. Each movie comprised of 30 frames acquired over 6s, with a cumulative does of ~35 electrons/Å2. Imaging was performed at a nominal magnification of 22,500X, with a pixel size of 1.31 Å/pixel at specimen level using a defocus ranging from 0.8μm to 4μm.
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