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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7506 | |||||||||
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Title | 1.15 A MicroED structure of GSNQNNF at 1.8 e- / A^2 | |||||||||
![]() | MicroED density map | |||||||||
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![]() | Amyloid fibril / prion / zinc binding / PROTEIN FIBRIL | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.15 Å | |||||||||
![]() | Hattne J / Shi D | |||||||||
![]() | ![]() Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM. Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen / ![]() Abstract: Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 175.4 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
Images | ![]() | 183 KB | ||
Filedesc metadata | ![]() | 4.7 KB | ||
Filedesc structureFactors | ![]() | 18.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6clnMC ![]() 7490C ![]() 7491C ![]() 7492C ![]() 7493C ![]() 7494C ![]() 7495C ![]() 7496C ![]() 7497C ![]() 7498C ![]() 7499C ![]() 7500C ![]() 7501C ![]() 7502C ![]() 7503C ![]() 7504C ![]() 7505C ![]() 7507C ![]() 7508C ![]() 7509C ![]() 7510C ![]() 7511C ![]() 7512C ![]() 6cl7C ![]() 6cl8C ![]() 6cl9C ![]() 6claC ![]() 6clbC ![]() 6clcC ![]() 6cldC ![]() 6cleC ![]() 6clfC ![]() 6clgC ![]() 6clhC ![]() 6cliC ![]() 6cljC ![]() 6clkC ![]() 6cllC ![]() 6clmC ![]() 6cloC ![]() 6clpC ![]() 6clqC ![]() 6clrC ![]() 6clsC ![]() 6cltC M: atomic model generated by this map C: citing same article ( |
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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 | MicroED density map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.34643 Å / Y: 0.36921 Å / Z: 0.3975 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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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: ACETATE ION
Macromolecule | Name: ACETATE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACT |
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Molecular weight | Theoretical: 59.044 Da |
Chemical component information | ![]() ChemComp-ACT: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 3 / 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 |
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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: 828 / Number diffraction images: 828 / Average exposure time: 2.1 sec. / Average electron dose: 0.00357 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | 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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.15 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystallography statistics | Number intensities measured: 7517 / Number structure factors: 1287 / Fourier space coverage: 79.7 / R sym: 0.225 / R merge: 0.225 / Overall phase error: 44.13 / Overall phase residual: 44.13 / Phase error rejection criteria: 0 / High resolution: 1.15 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.15 Å / Shell - Low resolution: 1.18 Å / Shell - Number structure factors: 115 / Shell - Phase residual: 66.98 / Shell - Fourier space coverage: 83.94 / Shell - Multiplicity: 6.2 |
-Atomic model buiding 1
Details | Electron scattering factors |
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Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 6.95 |
Output model | ![]() PDB-6cln: |