|Entry||Database: EMDB / ID: 3434|
|Title||Single-particle cryo-EM using alignment by classification (ABC):Lumbricus terrestris hemoglobin at near-atomic resolution|
|Keywords||Lumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin|
|Sample||Hemoglobin purified from Lumbricus Terrestris|
|Source||Lumbricus terrestris / invertebrata / Common Earthworm / Wikipedia|
|Map data||Worm hemoglobin cryo-EM 3D reconstruction sharpened and auto-masked|
|Method||single particle reconstruction, at 3.8 Å resolution|
|Authors||Afanasyev P / Linnemayr-Seer C / Ravelli RBG / Matadeen R / De Carlo S / Alewijnse B / Portugal RV / Pannu NS / Schatz M / van Heel M|
|Citation||IUCrJ, 2017, 4, 678-694|
IUCrJ, 2017, 4, 678-694 Yorodumi Papers
|Validation Report||PDB-ID: 5m3l|
SummaryFull reportAbout validation report
|Date||Deposition: May 11, 2016 / Header (metadata) release: Jun 15, 2016 / Map release: Jul 26, 2017 / Last update: Jul 26, 2017|
Downloads & links
|File||emd_3434.map.gz (map file in CCP4 format, 182251 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.11 Å|
CCP4 map header:
|File||emd_3434_msk.map ( map file in CCP4 format, 182251 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Space group number||1|
|Annotation details||Automatic mask applied to final 3D reconstruction|
-Entire Hemoglobin purified from Lumbricus Terrestris
|Entire||Name: Hemoglobin purified from Lumbricus Terrestris / Number of components: 1 / Oligomeric State: Dodecamer|
|Mass||Theoretical: 3.6 MDa|
-Component #1: protein, Hemoglobin
|Protein||Name: Hemoglobin / a.k.a: Erythrocruorin / Oligomeric Details: Dodecamer / Recombinant expression: No / Number of Copies: 12|
|Mass||Theoretical: 3.6 MDa|
|Source||Species: Lumbricus terrestris / invertebrata / Common Earthworm / Wikipedia|
|Source (natural)||Organ or tissue: hemolymph|
|Sample solution||Buffer solution: 0.1 M Tris-HCl buffer, 1 mM EDTA / pH: 7|
|Support film||Quantifoil grid (R2/2, Quantifoil Micro Tools GmbH)|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: 2.5 s blot time|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: May 25, 2014|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal) / Cs: 0.02 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1200 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 5235 / Bit depth: 16|
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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