+Open data
-Basic information
Entry | Database: PDB / ID: 7mrp | |||||||||
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Title | MicroED structure of lysozyme from milled crystals at 1.75A | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Lysozyme | |||||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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: 1.75 Å | |||||||||
Authors | Martynowycz, M.W. / Gonen, T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be Published Title: Preparing crystalline lamellae by focused ion-beam milling for microcrystal electron diffraction (MicroED) experiments Authors: Martynowycz, M.W. / Gonen, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mrp.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mrp.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/7mrp ftp://data.pdbj.org/pub/pdb/validation_reports/mr/7mrp | HTTPS FTP |
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-Related structure data
Related structure data | 23957MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 | ChemComp-NA / #3: Chemical | ChemComp-CL / | #4: 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 | Value: 0.0143 MDa / Experimental value: NO |
Source (natural) | Organism: Gallus gallus (chicken) |
Buffer solution | pH: 4.7 |
Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Data collection
Microscopy | Model: TFS TALOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal defocus min: 0 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 85 K / Temperature (min): 77 K |
Image recording | Average exposure time: 1 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 1500 / Num. of grids imaged: 1 / Num. of real images: 1500 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
EM diffraction | Camera length: 2100 mm / Tilt angle list: -30,30 |
EM diffraction shell | Resolution: 1.75→34.18 Å / Fourier space coverage: 100 % / Multiplicity: 25 / Num. of structure factors: 12144 / Phase residual: 18 ° |
EM diffraction stats | Fourier space coverage: 100 % / High resolution: 1.75 Å / Num. of intensities measured: 305349 / Num. of structure factors: 12144 / Phase error: 18 ° / Phase residual: 19 ° / Phase error rejection criteria: none / Rmerge: 0.23 |
Reflection | Biso Wilson estimate: 27.13 Å2 |
-Processing
Software |
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 77.33 Å / B: 77.33 Å / C: 38.11 Å / Space group name: P43212 / Space group num: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.75 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Algorithm: FOURIER SPACE / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 25 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: LL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5K7O | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 1.75→34.04 Å / SU ML: 0.2792 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6143 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: 26.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→34.04 Å
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Refine LS restraints |
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LS refinement shell |
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