+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6422 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of GroEL | |||||||||
Map data | CryoEM structure of GroEL | |||||||||
Sample |
| |||||||||
Keywords | GroEL | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Roh SH / Hryc C / Chiu W | |||||||||
Citation | Journal: To Be Published Title: CryoEM of GroEL Authors: Roh SH / Hryc C / Chiu W | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6422.map.gz | 49.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6422-v30.xml emd-6422.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | 400_6422.gif 80_6422.gif | 109.5 KB 6.5 KB | ||
Others | emd_6422_additional_1.map.gz emd_6422_half_map_1.map.gz emd_6422_half_map_2.map.gz | 41 MB 41 MB 41 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6422 | HTTPS FTP |
-Validation report
Summary document | emd_6422_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6422_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6422_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6422 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6422.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | CryoEM structure of GroEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Supplemental map: emd 6422 additional 1.map
File | emd_6422_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: emd 6422 half map 1.map
File | emd_6422_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: emd 6422 half map 2.map
File | emd_6422_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Wild type GroEL
Entire | Name: Wild type GroEL |
---|---|
Components |
|
-Supramolecule #1000: Wild type GroEL
Supramolecule | Name: Wild type GroEL / type: sample / ID: 1000 / Oligomeric state: 14-mer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 800 KDa / Theoretical: 800 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: LEICA EM GP / Method: Blot once for 5 seconds. |
-Electron microscopy
Microscope | JEOL 3200FS |
---|---|
Temperature | Average: 86 K |
Specialist optics | Energy filter - Name: in-column omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV |
Date | Aug 8, 2014 |
Image recording | Category: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 300 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.3 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: particle-based |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 40000 |