[English] 日本語
![](img/lk-miru.gif)
- EMDB-21203: 1.4A damaged structure of GSNQNNF used to determine initial phase... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-21203 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.4A damaged structure of GSNQNNF used to determine initial phases from radiation damage | |||||||||
![]() | 2mFo-Fc map for the damaged GSNQNNF structure refined from the solved low-dose structure that had initially determined experimental phases | |||||||||
![]() |
| |||||||||
![]() | MicroED / damage / phasing / RIP / protein fibril | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | electron crystallography / cryo EM | |||||||||
![]() | Martynowycz MW / Hattne J | |||||||||
![]() | ![]() Title: Experimental Phasing of MicroED Data Using Radiation Damage. Authors: Michael W Martynowycz / Johan Hattne / Tamir Gonen / ![]() Abstract: We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present ...We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present an example of an experimentally phased structure using only MicroED data. The structure of a seven-residue peptide is solved starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous-rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a "low-dose dataset." The data from the second pass were similarly merged to form a "damaged dataset." Differences between these two datasets were used to identify a single heavy-atom site from a Patterson difference map, and initial phases were generated. Finally, the structure was completed by iterative cycles of modeling and refinement. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 157.4 KB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.3 KB 13.3 KB | Display Display | ![]() |
Images | ![]() | 82.8 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Filedesc structureFactors | ![]() | 59.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 643 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 642.5 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 2mFo-Fc map for the damaged GSNQNNF structure refined from the solved low-dose structure that had initially determined experimental phases | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.40667 Å / Y: 0.44281 Å / Z: 0.4405 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Synthetic proto-filament
Entire | Name: Synthetic proto-filament |
---|---|
Components |
|
-Supramolecule #1: Synthetic proto-filament
Supramolecule | Name: Synthetic proto-filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 899.141 Da |
-Macromolecule #1: GSNQNNF
Macromolecule | Name: GSNQNNF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 779.756 Da |
Sequence | String: GSNQNNF |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: ACETATE ION
Macromolecule | Name: ACETATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ACT |
---|---|
Molecular weight | Theoretical: 59.044 Da |
Chemical component information | ![]() ChemComp-ACT: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | electron crystallography |
Aggregation state | 3D array |
-
Sample preparation
Concentration | 10 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 6 Component:
| |||||||||
Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | Hanging drop. |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 736 / Number diffraction images: 736 / Average exposure time: 2.1 sec. / Average electron dose: 0.00588 e/Å2 / Details: Images collected as a movies. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 730 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Details | Rolling shutter and binned by 2. |
---|---|
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES |
Crystallography statistics | Number intensities measured: 6314 / Number structure factors: 722 / Fourier space coverage: 78.1 / R sym: 0.21 / R merge: 0.199 / Overall phase error: 26 / Overall phase residual: 26 / Phase error rejection criteria: 0 / High resolution: 1.4 Å Details: Model from the low-dose set refined against the damage dataset without any changes. Shell - Shell ID: 1 / Shell - High resolution: 1.4 Å / Shell - Low resolution: 13.97 Å / Shell - Number structure factors: 722 / Shell - Phase residual: 26 / Shell - Fourier space coverage: 78.1 / Shell - Multiplicity: 8.7 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-7 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 5 |
Output model | ![]() PDB-6vhc: |