- EMDB-30683: Krios G4 apoferritin test with K3/BioQuantum SerialEM BIS 3x3x1 -
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Basic information
Entry
Database: EMDB / ID: EMD-30683
Title
Krios G4 apoferritin test with K3/BioQuantum SerialEM BIS 3x3x1
Map data
Sharpened apoferritin map
Sample
Complex: apoferritin
Function / homology
Function and homology information
Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / immune response / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function
Journal: Microscopy (Oxf) / Year: 2021 Title: Cryo-EM performance testing of hardware and data acquisition strategies. Authors: Radostin Danev / Haruaki Yanagisawa / Masahide Kikkawa / Abstract: The increasing popularity and adoption rate of cryo-electron microscopy (cryo-EM) is evidenced by a growing number of new microscope installations around the world. The quality and reliability of the ...The increasing popularity and adoption rate of cryo-electron microscopy (cryo-EM) is evidenced by a growing number of new microscope installations around the world. The quality and reliability of the instruments improved dramatically in recent years, but site-specific issues or unnoticed problems during installation could undermine productivity. Newcomers to the field may also have limited experience and/or low confidence in the capabilities of the equipment or their own skills. Therefore, it is recommended to perform an initial test of the complete cryo-EM workflow with an 'easy' test sample, such as apoferritin, before starting work with real and challenging samples. Analogous test experiments are also recommended for the quantification of new data acquisition approaches or imaging hardware. Here, we present the results from our initial tests of a recently installed Krios G4 electron microscope equipped with two latest generation direct electron detector cameras-Gatan K3 and Falcon 4. Three beam-image shift-based data acquisition strategies were also tested. We detail the methodology and discuss the critical parameters and steps for performance testing. The two cameras performed equally, and the single- and multi-shot per-hole acquisition schemes produced comparable results. We also evaluated the effects of environmental factors and optical flaws on data quality. Our results reaffirmed the exceptional performance of the software aberration correction in Relion in dealing with severe coma aberration. We hope that this work will help cryo-EM teams in their testing and troubleshooting of hardware and data collection approaches.
History
Deposition
Nov 17, 2020
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Header (metadata) release
Dec 2, 2020
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Map release
Dec 2, 2020
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Update
Mar 16, 2022
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Current status
Mar 16, 2022
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10559 (Title: Krios G4 apoferritin test with K3/BioQuantum SerialEM BIS 3x3x1 Data size: 659.0 Data #1: Unaligned multi-frame non-gain-normalized movies in LZW compressed TIFF format [micrographs - multiframe])
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