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- PDB-7dln: Structure of lysozyme obtained on SSRF using serial synchrotron c... -
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Basic information
Entry | Database: PDB / ID: 7dln | ||||||
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Title | Structure of lysozyme obtained on SSRF using serial synchrotron crystallography | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhao, F.Z. | ||||||
![]() | ![]() Title: Structure of lysozyme obtained on SSRF using serial synchrotron crystallography Authors: Zhao, F.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.9 KB | Display | ![]() |
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PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.3 KB | Display | ![]() |
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Full document | ![]() | 415.3 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 193lS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: sodium chloride, PEG20000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→34.25 Å / Num. obs: 6887 / % possible obs: 99.26 % / Redundancy: 14.17 % / Biso Wilson estimate: 77.29 Å2 / CC1/2: 0.885 / R split: 0.2752 / Net I/σ(I): 3.98 |
Reflection shell | Resolution: 2.15→2.23 Å / Mean I/σ(I) obs: 2.45 / Num. unique obs: 659 / CC1/2: 0.577 / R split: 0.5341 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 193L Resolution: 2.15→34.244 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.48 / Stereochemistry target values: ML
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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 max: 123.47 Å2 / Biso mean: 77.2344 Å2 / Biso min: 64.47 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→34.244 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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