[English] 日本語
Yorodumi- EMDB-41933: CryoEM map of horse spleen apoferritin determined as a reference ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41933 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM map of horse spleen apoferritin determined as a reference for benchmarking square and rectangular apertures for cryo-EM | |||||||||
Map data | Main map, Gatan K3 dataset using standard round beam (50 micron aperture) for comparison with square and rectangular aperture results. Sharpened with B-factor of 52.6. | |||||||||
Sample |
| |||||||||
Keywords | Apo-ferritin / METAL BINDING PROTEIN | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.81 Å | |||||||||
Authors | Brown HG / Hanssen E | |||||||||
Funding support | Australia, 1 items
| |||||||||
Citation | Journal: Nat Methods / Year: 2024 Title: Square condenser apertures for square cameras in low-dose transmission electron microscopy. Authors: Hamish G Brown / Dan Smith / Benjamin C Wardle / Eric Hanssen / Abstract: In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam- ...In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41933.map.gz | 350.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41933-v30.xml emd-41933.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41933_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_41933.png | 268.5 KB | ||
Masks | emd_41933_msk_1.map | 371.3 MB | Mask map | |
Filedesc metadata | emd-41933.cif.gz | 5.2 KB | ||
Others | emd_41933_half_map_1.map.gz emd_41933_half_map_2.map.gz | 343.8 MB 343.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41933 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41933 | HTTPS FTP |
-Validation report
Summary document | emd_41933_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41933_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41933_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | emd_41933_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41933 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41933 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_41933.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main map, Gatan K3 dataset using standard round beam (50 micron aperture) for comparison with square and rectangular aperture results. Sharpened with B-factor of 52.6. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.655 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_41933_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A
File | emd_41933_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map B
File | emd_41933_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Apoferritin from equine spleen
Entire | Name: Apoferritin from equine spleen |
---|---|
Components |
|
-Supramolecule #1: Apoferritin from equine spleen
Supramolecule | Name: Apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purchased from Sigma Aldrich product number A3641 |
---|---|
Source (natural) | Organism: Equus caballus (horse) |
Molecular weight | Theoretical: 481.2 KDa |
-Macromolecule #1: Apoferritin from equine spleen
Macromolecule | Name: Apoferritin from equine spleen / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Equus caballus (horse) |
Sequence | String: SQIRQNYSTE VEAAVNRLV N LYLRASYT YL SLGFYFD RDD VALEGV CHFF RELAE EKREG AERL LKMQNQ RGG RALFQDL QK PSQDEWGT T LDAMKAAIV LEKSLNQALL DLHALGSAQ A DPHLCDFL ES HFLDEEV KLI KKMGDH LTNI QRLVG SQAGL GEYL FERLTL K |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 35 mg/mL |
---|---|
Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Details: Quorum Glocube |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
Details | Solution purchased from Sigma Aldrich and no further purification |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3111 / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |