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Epsilon15 asymmetric reconstruction using conventional cryo-EM
by single particle reconstruction, at 13 A resolution
#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5209 |
|---|---|
| Title | Epsilon15 asymmetric reconstruction using conventional cryo-EM |
| Map | asymmetric reconstruction of epsilon15 from conventional cryoEM particles |
| Sample | Epsilon15 |
| Keywords |  Electron microscopy, phase plate, Bacteriophage, epsilon15 |
| Authors | Murata K, Liu X, Danev R, Jakana J, Schmid MF, King J, Nagayama K, Chiu W |
| Date | Deposition: 2010-07-01, Header release: 2010-07-19, Map release: 2010-09-01, Last update: 2011-07-08 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Structure, Vol. 18, Issue 8, Page 903-12, Year 2010 |
|---|---|
| Title | Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. |
| Authors | Kazuyoshi Murata, Xiangan Liu, Radostin Danev, Joanita Jakana, Michael F Schmid, Jonathan King, Kuniaki Nagayama, Wah Chiu National Center for Macromolecular Imaging, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. |
| Keywords | Bacteriophages (ultrastructure), Bacteriorhodopsins (ultrastructure, 53026-44-1), Cryoelectron Microscopy (methods), Crystallography (methods), Electron Microscope Tomography (methods), Epsilonproteobacteria (virology), Image Processing, Computer-Assisted (methods), Microscopy, Phase-Contrast (methods), Models, Molecular |
| Links | PII: S0969-2126(10)00235-2, DOI: 10.1016/j.str.2010.06.006, PubMed: 20696391, PMC: PMC2925294 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5209.map ( map file in CCP4 format, 764413 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 1123.2 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.95 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | asymmetric reconstruction of epsilon15 from conventional cryoEM particles | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Epsilon15 |
|---|---|
| Number of Components | 6 |
| Theoretical Mass | 0.5MDa |
| Details | The sample was monodisperse |
| Component #1: virus - bacteriophage | |
| Scientific name | epsilon15 |
| Common Name | bacteriophage |
| Scientific Name of Species | epsilon15 |
| Common Name of Species | bacteriophage |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 590 Host Species: Salmonella Host Category: BACTERIA(EUBACTERIA) |
| Shell | Id: 1 , Diameter: 700 A, T Number: 7 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | Quantifoil R2/2 grid |
|---|---|
| Specimen State | particle |
| Buffer | Details: 10 mM Tris pH7.5, 25 mM NaCl and 5 mM MgCl2 pH: 7.5 |
| Vitrification | |
| Method | Blot for 2 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: vitrobot |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | JEOL 2200FS |
| Date | 01-DEC-2009 |
| Details | Weak beam illumination |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 75000, Calibrated: 75000 |
| Nominal Cs | 4.3 mm |
| Imaging Mode | BRIGHT FIELD |
| Energy Filter | Energy Filter: JEOL , Energy Window: 0-20 eV |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 90 K |
| Camera | |
| Detector | Tietz 4K X 4K CCD camera |
| Image Acquisition | |
| Number of Digital Images | 722 |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Cross-common lines |
| Software | MPSA |
| CTF Correction | each micrograph |
| Details | the map was reconstructed with ctf correction. |
| Resolution By Author | 13 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 17800 |
| Details | The particles were selected using the consistency criterion of MPSA |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5209.xml (7.2 KB) | ||
|---|---|---|---|
| Map data | emd_5209.map.gz (97.7 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5209 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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