+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10736 | |||||||||
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Title | Lumazine Synthase | |||||||||
Map data | Reconstruction of Lumazine Synthase, sharpened and filtered at 2 angstroms | |||||||||
Sample |
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Biological species | Aquifex aeolicus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
Authors | Bhella D / Streetley J / Clarke M / Cowton V / Patel A / Bammes B / Hosogi N | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Biophys Rev / Year: 2019 Title: Cryo-electron microscopy: an introduction to the technique, and considerations when working to establish a national facility. Authors: David Bhella / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10736.map.gz | 227.1 MB | EMDB map data format | |
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Header (meta data) | emd-10736-v30.xml emd-10736.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10736_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10736.png | 251.7 KB | ||
Masks | emd_10736_msk_1.map | 244.1 MB | Mask map | |
Others | emd_10736_half_map_1.map.gz emd_10736_half_map_2.map.gz | 193.5 MB 193.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10736 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10736 | HTTPS FTP |
-Validation report
Summary document | emd_10736_validation.pdf.gz | 541.2 KB | Display | EMDB validaton report |
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Full document | emd_10736_full_validation.pdf.gz | 540.3 KB | Display | |
Data in XML | emd_10736_validation.xml.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10736 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10736 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10384 (Title: Cryo-EM structure of Lumazine Synthase / Data size: 3.0 TB Data #1: Frame aligned multi-frame movies of Lumazine Synthase imaged on a CryoARM300 and DE64 [micrographs - multiframe]) EMPIAR-10385 (Title: Cryo-EM structure of Lumazine Synthase / Data size: 6.8 TB Data #1: Frame aligned multi-frame movies of Lumazine Synthase imaged on a CryoARM300 and DE64 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10736.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Lumazine Synthase, sharpened and filtered at 2 angstroms | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.597 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10736_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_10736_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_10736_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Icosahedral complex of Lumazine Synthase
Entire | Name: Icosahedral complex of Lumazine Synthase |
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Components |
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-Supramolecule #1: Icosahedral complex of Lumazine Synthase
Supramolecule | Name: Icosahedral complex of Lumazine Synthase / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | Purified by immobilised metal affinity chromatography. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 13.0 µm / Digitization - Frames/image: 1-41 / Number grids imaged: 1 / Number real images: 1199 / Average exposure time: 10.0 sec. / Average electron dose: 1.66 e/Å2 Details: Images were acquired at 141 FPS with 2 x binning and electron counting. A total of 41 summed frames were written out. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 200000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |