Aligned movie frames (.mrcs extension), aligned-averaged micrographs (.mrc extension) and particle coordinates (.box extension)

MRC

1028

(4096, 4096)

32 BIT FLOAT

(1.14, 1.14)

This directory contains selected aligned movie frames (.mrcs extension) and their corresponding aligned-averaged micrographs (.mrc extension) and particle coordinates (.box extension) files which went into HPeV3 reconstruction. These were collected on a 300 kV Titan Krios with Falcon II detector at NECEN with an electron dose of 35-38 electrons per square Ångstrom per second. The nominal magnification was 59000 X. The pixel size was 1.14 Ångstrom per pixel. The Cs value was 0.01 mm. The movie frames were aligned using motion_corr software (Li et al. (2013) Electron counting and beam-induced motion correction enables near atomic resolution single particle cryoEM. Nature Methods, 10, 584-590), the particles were automatically selected using ethan software (Kivioja et al. (2000) Local average intensity-based method for identifying spherical particles in electron micrographs. J Struct Biol. 131:126-34). the bad or wrong particle coordinates were deselected in boxer (Ludtke et al. EMAN: semiautomated software for high-resolution single-particle reconstructions.J Struct Biol. 1999 Dec 1;128(1):82-97) .and the reconstruction was done in Relion version1.3. (Scheres SH. (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 180(3):519-30).

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micrographs - multiframe

RAW FEI

46228

(4096, 4096)

32 BIT FLOAT

(1.14, 1.14)

This directory contains all the data that were collected on the same sample in the same two data collection sessions. Unlike the aligned_micrographs_directory, this contains all of the micrographs that were rejected by us, including those that were considered too drifted, too thick, too astigmatic etc. for processing. We hope that this will provide data for those that want to improve algorithms using such images. We had to use a renaming script in order to utilise these data. It is available on request.
These are unaligned movie frames of HPeV3 virus capsids collected on a Titan Krios 300 kV with a Falcon II detector at NeCEN, Leiden. There are 7 frames per micrograph labelled from XXX_n0.raw to XXX_n6.raw. The Cs value is 0.01 mm. The sampling is 1.14 Å per pixel. The nominal magnification is 59000 X. Electron dose of 35-38 electrons per squared angstrom per second is used.
The raw files can be converted to mrc using many different programs (xmipp, em2em etc), one of them is raw2mrc script in imod:

raw2mrc -o 49 -x 4096 -y 4096 -t long -c

The number of ultimately selected images is 6604.

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