[English] 日本語
Yorodumi- EMDB-21202: 1.4A low-dose structure of GSNQNNF determined from initial phases... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21202 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.4A low-dose structure of GSNQNNF determined from initial phases generated using radiation damage | |||||||||
Map data | 2mFo-dFc map for GSNQNNF built from initial phases generated by radiation damage | |||||||||
Sample |
| |||||||||
Keywords | MicroED / damage / phasing / RIP / protein fibril | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.4 Å | |||||||||
Authors | Martynowycz MW / Hattne J | |||||||||
Citation | Journal: Structure / Year: 2020 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 |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21202.map.gz | 157.5 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21202-v30.xml emd-21202.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_21202.png | 94.5 KB | ||
Filedesc metadata | emd-21202.cif.gz | 5 KB | ||
Filedesc structureFactors | emd_21202_sf.cif.gz | 60.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21202 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21202 | HTTPS FTP |
-Validation report
Summary document | emd_21202_validation.pdf.gz | 650.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_21202_full_validation.pdf.gz | 650.4 KB | Display | |
Data in XML | emd_21202_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | emd_21202_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21202 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21202 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21202.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
---|---|
Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Concentration | 10 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 6 Component:
| |||||||||
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. |
-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 movies. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
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.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 |
---|---|
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 2 |
Output model | PDB-6vhb: |