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ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by differential Evolution with Spectral Self-adaptation), which is a new high-resolution single-particle orientation refinement method based on spectrally self-adapting common lines
by single particle reconstruction, at 7 A resolution
#1: Surface view with section colored by density value, Surface level: 0.013, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.013, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-1oel, Surface level: 0.013, Made by UCSF CHIMERA
#4: Surface view with fitted model, atomic models: PDB-1oel, Surface level: 0.013, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1587 |
|---|---|
| Title | ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by differential Evolution with Spectral Self-adaptation), which is a new high-resolution single-particle orientation refinement method based on spectrally self-adapting common lines |
| Map | ab initio 3D reconstruction of GroEL using 3DESS |
| Sample | GroEL data provided by National Resource for Automated Molecular Microscopy |
| Keywords |  GroEL, common lines, spectral self-adaptation |
| Authors | Elmlund D, Elmlund H |
| Date | Deposition: 2008-12-15, Header release: 2008-12-15, Map release: 2009-04-01, Last update: 2012-10-24 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.013, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.013, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1oel, Surface level: 0.013, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-1oel, Surface level: 0.013, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Struct. Biol., Vol. 167, Issue 1, Page 83-94, Year 2009 |
|---|---|
| Title | High-resolution single-particle orientation refinement based on spectrally self-adapting common lines. |
| Authors | Dominika Elmlund, Hans Elmlund Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, Novum, SE-141 87 Huddinge, Sweden. |
| Keywords | Algorithms, Imaging, Three-Dimensional (methods), Microscopy, Electron (methods) |
| Links | PII: S1047-8477(09)00116-6, DOI: 10.1016/j.jsb.2009.04.009, PubMed: 19410651 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1587.map ( map file in CCP4 format, 10978 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 228.2 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.63 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | ab initio 3D reconstruction of GroEL using 3DESS | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | GroEL data provided by National Resource for Automated Molecular Microscopy |
|---|---|
| Number of Components | 1 |
| Oligomeric State | 14-meric and d7 symmetric GroEL |
| Details | All sample details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 |
| Component #1: cellular-component - GroEL | |
| Scientific name | GroEL |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Recombinant expression | Yes |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Details | All imaging details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 120 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
| Image Acquisition | |
| Details | All image processing details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | cross-common lines |
| Software | Evol-Align |
| CTF Correction | each micrograph, phase flipping only |
| Resolution By Author | 7 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | All experimental details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 |
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