The initial model served as a reference in a three-dimensional (3D) classification, where the best-looking class containing 267,000 particles was selected, the particles were unbinned 2 times (220-pixel box size, 1.302 Å pixel−1) and refined to 3.3 Å with C2 symmetry ...
Particles with a box size of 256 pixels (px) and a px size of 1.86 Å/px were extracted with helical priors and 16 asymmetrical units, which were used for the entire processing. The next steps consisted of two rounds of 2D classification into 200 and 100 classes, respectively, aimed...
6)51. Briefly, particles were template-picked and extracted from micrographs with a box size of 224 pix initially binned by 4 (4.224 Å/pix). Ab initio reconstructions were performed with curated, 2D classified particles with a bin of 2 (2.112 Å/pix). The best reconstruction ...
2. Extract Mics. From the builder in CryoSPARC, select theExtract Mics.job to extract the particles. This job expects: Inputs: Output of Patch CTF job and Output of Import Particles job Extraction box size (pix): Box size in pixels, by default 256 ...
Use the parse_ctf_star or parse_ctf_csparc command to extract the relevant CTF parameters from a .star file or a .cs file, respectively.Example usage for a .star file:$ cryodrgn parse_ctf_star particles.star -o ctf.pkl If the box size and Angstrom/pixel values are not included in ...
In the single particle selection, usually use a certain radius size of the circle for selection, when extracting (Extract), the extraction box is usually selected not less than the diameter of the circle square box for frame. Therefore, the size of the single-grain image we are dealing with...
Full size image VirB4unboundis also composed of dimers that have essentially the same structure as the VirB4central–VirB4outsidedimer in the T4SS (Cα root mean squared deviation (r.m.s.d.) 1.2 Å; Extended Data Fig.6a,f). However, in this unbound structure, part of the dimer...
The selected particles were re-centered and the box size was reduced to 182x182 pixels. Particles were re-centered again and further 3D-classified into 5 classes, of which one class containing 200,405 particles was selected for further processing. Subsequently, this class separated into 4 ...
In the single particle selection, usually use a certain radius size of the circle for selection, when extracting (Extract), the extraction box is usually selected not less than the diameter of the circle square box for frame...
Proteins were visualized by chemiluminescence using a G:Box (Syngene). To quantify Aβ in brain extracts, the staining intensity of the Aβ band in the fibril extract was compared to a standard series containing 1.56 to 100 μg/mL recombinant Aβ(1–40). The band intensity was ...