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Yorodumi- PDB-6lav: MicroED structure of lysozyme at 1.73A determained using crystal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lav | |||||||||||||||
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Title | MicroED structure of lysozyme at 1.73A determained using crystal lamellas prepared by focused ion beam milling | |||||||||||||||
Components | Lysozyme C | |||||||||||||||
Keywords | HYDROLASE / Lysozyme / MicroED / Focused Ion Beam / crystal lamella | |||||||||||||||
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: 1.73 Å | |||||||||||||||
Authors | Zhou, H. / Luo, Z. / Li, X. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Using focus ion beam to prepare crystal lamella for electron diffraction. Authors: Heng Zhou / Zhipu Luo / Xueming Li / Abstract: Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the ...Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope. | |||||||||||||||
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 | 6lav.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lav.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lav_validation.pdf.gz | 897.6 KB | Display | wwPDB validaton report |
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Full document | 6lav_full_validation.pdf.gz | 897.1 KB | Display | |
Data in XML | 6lav_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6lav_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6lav ftp://data.pdbj.org/pub/pdb/validation_reports/la/6lav | HTTPS FTP |
-Related structure data
Related structure data | 0864MC 0865C 6lawC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: lysozyme / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Gallus gallu (chicken) |
Buffer solution | pH: 4.5 |
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: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 0.057 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
EM diffraction | Camera length: 1200 mm |
EM diffraction shell | Resolution: 1.7→1.76 Å / Fourier space coverage: 79.1 % / Multiplicity: 9.7 / Num. of structure factors: 1002 / Phase residual: 1 ° |
EM diffraction stats | Fourier space coverage: 89 % / High resolution: 1.7 Å / Num. of intensities measured: 121300 / Num. of structure factors: 11548 / Phase error: 0 ° / Phase residual: 1 ° / Phase error rejection criteria: 60 / Rmerge: 0.281 / Rsym: 0.281 |
Detector | Date: Feb 2, 2018 |
-Processing
Software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 78.99 Å / B: 78.99 Å / C: 37.89 Å / Space group name: P43212 / Space group num: 96 | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.73 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | ||||||||||||||||||||||||
Refinement | Resolution: 1.73→14.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.69 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.147 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 90.95 Å2 / Biso mean: 28.358 Å2 / Biso min: 12.1 Å2
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Refinement step | Cycle: final / Resolution: 1.73→14.67 Å
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LS refinement shell | Resolution: 1.732→1.777 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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