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- EMDB-21202: 1.4A low-dose structure of GSNQNNF determined from initial phases... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21202 | |||||||||
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Title | 1.4A low-dose structure of GSNQNNF determined from initial phases generated using radiation damage | |||||||||
![]() | 2mFo-dFc map for GSNQNNF built from initial phases generated by radiation damage | |||||||||
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![]() | MicroED / damage / phasing / RIP / protein fibril | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.4 Å | |||||||||
![]() | 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 157.5 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
Images | ![]() | 94.5 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Filedesc structureFactors | ![]() | 60.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 2mFo-dFc map for GSNQNNF built from initial phases generated by radiation damage | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.40667 Å / Y: 0.44281 Å / Z: 0.4405 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Synthetic proto-filament
Entire | Name: Synthetic proto-filament |
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Components |
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-Supramolecule #1: Synthetic proto-filament
Supramolecule | Name: Synthetic proto-filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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 |
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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 |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: ACETATE ION
Macromolecule | Name: ACETATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ACT |
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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 |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 6 Component:
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Grid | Model: Quantifoil R2/2 / 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. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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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 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 |
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Image processing
Details | Rolling shutter and binned by 2. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.4 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
Crystallography statistics | Number intensities measured: 6026 / Number structure factors: 713 / Fourier space coverage: 77.2 / R sym: 0.219 / R merge: 0.208 / Overall phase error: 24 / Overall phase residual: 24 / Phase error rejection criteria: 0 / High resolution: 1.4 Å Details: Initial phases were obtained by taking the difference between the low-dose and damaged set, and locating the zinc atom to generate experimental phases. Shell - Shell ID: 1 / Shell - High resolution: 14.0 Å / Shell - Low resolution: 1.4 Å / Shell - Number structure factors: 713 / Shell - Phase residual: 24 / Shell - Fourier space coverage: 77.2 / Shell - Multiplicity: 8.5 |
-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 |
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Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 2 |
Output model | ![]() PDB-6vhb: |