+Open data
-Basic information
Entry | Database: PDB / ID: 6s2n | ||||||
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Title | Hen egg-white lysozyme by serial electron diffraction | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / HEWL / serial crystallography | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.8 Å | ||||||
Authors | Buecker, R. / Mehrabi, P. / Schulz, E.C. / Hogan-Lamarre, P. | ||||||
Citation | Journal: Nat Commun / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s2n.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s2n.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s2n_validation.pdf.gz | 610.7 KB | Display | wwPDB validaton report |
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Full document | 6s2n_full_validation.pdf.gz | 612.7 KB | Display | |
Data in XML | 6s2n_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 6s2n_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/6s2n ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s2n | HTTPS FTP |
-Related structure data
Related structure data | 10090MC 6s2oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10542 (Title: Serial electron diffraction from hen egg-white lysozyme Data size: 17.7 Data #1: Serial electron diffraction raw data from Lysozyme nano-crystals, taken with dose fractionation [diffraction images]) |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Lysozyme / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Gallus gallus (chicken) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: DIFFRACTION / C2 aperture diameter: 5 µm |
Image recording | Average exposure time: 0.006 sec. / Electron dose: 2 e/Å2 / Film or detector model: OTHER / Num. of grids imaged: 1 |
EM diffraction | Camera length: 1570 mm / Tilt angle list: 0 |
EM diffraction shell | Resolution: 30→0.1 Å / Fourier space coverage: 1 % / Multiplicity: 1 / Num. of structure factors: 1 / Phase residual: 1 ° |
EM diffraction stats | Details: Data reduction/reconstruction using X-ray crystallographic software (CrystFEL, Phaser, cctbx.refine, Coot) Fourier space coverage: 80.8 % / High resolution: 1.8 Å / Num. of intensities measured: 16139 / Num. of structure factors: 9444 / Phase error: 29.4 ° / Phase residual: 1 ° / Phase error rejection criteria: 0 / Rmerge: 0.23 / Rsym: 0.23 |
Reflection | Biso Wilson estimate: 9.52 Å2 |
-Processing
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 78.1 Å / B: 78.1 Å / C: 38 Å / Space group name: P43212 / Space group num: 96 | ||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||
Refinement | Resolution: 1.8→55.93 Å / SU ML: 0.3568 / Cross valid method: FREE R-VALUE / σ(F): 1.62 / Phase error: 30.7521 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.48 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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