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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10090 | |||||||||
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Title | Hen egg-white lysozyme by serial electron diffraction | |||||||||
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Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.8 Å | |||||||||
![]() | Buecker R / Mehrabi P / Schulz EC / Hogan-Lamarre P | |||||||||
![]() | ![]() Title: Serial protein crystallography in an electron microscope. Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / ...Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / R J Dwayne Miller / ![]() ![]() Abstract: Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample ...Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation. | |||||||||
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 | ![]() | 788.4 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 114.9 KB | ||
Filedesc structureFactors | ![]() | 277.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s2nMC ![]() 6s2oC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 17.7 Data #1: Serial electron diffraction raw data from Lysozyme nano-crystals, taken with dose fractionation [diffraction images]) |
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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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Voxel size | X: 0.43944 Å / Y: 0.43944 Å / Z: 0.39583 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 : Lysozyme
Entire | Name: Lysozyme |
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Components |
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-Supramolecule #1: Lysozyme
Supramolecule | Name: Lysozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Lysozyme C
Macromolecule | Name: Lysozyme C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.33116 KDa |
Sequence | String: KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDIT ASVNCAKKIV SDGNGMNAWV AWRNRCKGTD VQAWIRGCRL |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 60 / 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 | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: OTHER / Number grids imaged: 1 / Average exposure time: 0.006 sec. / Average electron dose: 2.0 e/Å2 |
Tilt angle | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 5.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Camera length: 1570 mm |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystal parameters | Unit cell - A: 78.1 Å / Unit cell - B: 78.1 Å / Unit cell - C: 38 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P43212 |
Crystallography statistics | Number intensities measured: 16139 / Number structure factors: 9444 / Fourier space coverage: 80.8 / R sym: 0.23 / R merge: 0.23 / Overall phase error: 29.4 / Overall phase residual: 1 / Phase error rejection criteria: 0 / High resolution: 1.8 Å Details: Data reduction/reconstruction using X-ray crystallographic software (CrystFEL, Phaser, cctbx.refine, Coot) Shell - Shell ID: 1 / Shell - High resolution: 30.0 Å / Shell - Low resolution: 0.1 Å / Shell - Number structure factors: 1 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 1 / Shell - Multiplicity: 1 |