|Entry||Database: EMDB / ID: 0144|
|Title||Human apo-ferritin reconstructed in RELION-3.0|
|Map data||Human apo-ferritin reconstructed in RELION-3.0|
|Source||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / 1.65 Å resolution|
|Authors||Zivanov J / Nakane T / Hagen WJH / Scheres SHW|
|Citation||Journal: Elife / Year: 2018|
Title: New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Authors: Jasenko Zivanov / Takanori Nakane / Björn O Forsberg / Dari Kimanius / Wim Jh Hagen / Erik Lindahl / Sjors Hw Scheres
Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory ...Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions.
|Date||Deposition: Jul 26, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Dec 26, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_0144.map.gz (map file in CCP4 format, 186625 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.814 Å|
CCP4 map header:
-Entire human apo-ferritin
|Entire||Name: human apo-ferritin / Number of components: 1|
-Component #1: protein, human apo-ferritin
|Protein||Name: human apo-ferritin / Recombinant expression: No|
|Mass||Theoretical: 440 kDa|
|Source||Species: Escherichia coli (E. coli)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
Details: Used beam shift to collect seven images within one 1.2um Quantifoil hole. Used active beamtilt compensation in TEM microscope software.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 1255|
|Raw data||EMPIAR-10200 (Title: Human apo-ferritin reconstructed in RELION-3.0 / Data size: 191.5 |
Data #1: Unaligned multi-frame micrographs (in non-gain-corrected TIFF) of human apo-ferritin [micrographs - multiframe])
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