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Open data
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Basic information
Entry | Database: PDB / ID: 8dct | |||||||||||||||
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Title | Lysozyme cluster 3 dual apo structure | |||||||||||||||
![]() | Lysozyme C | |||||||||||||||
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Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Soares, A.S. / Yamada, Y. / Jakoncic, J. / Schneider, D.K. / Bernstein, H.J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Serial crystallography with multi-stage merging of thousands of images. Authors: Soares, A.S. / Yamada, Y. / Jakoncic, J. / McSweeney, S. / Sweet, R.M. / Skinner, J. / Foadi, J. / Fuchs, M.R. / Schneider, D.K. / Shi, W. / Andi, B. / Andrews, L.C. / Bernstein, H.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dcuC ![]() 8dcvC ![]() 8dcwC ![]() 4n8zS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NDG.gif)
![](data/chem/img/NDG.gif)
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#5: Sugar | ChemComp-NDG / ![]() |
-Non-polymers , 4 types, 220 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||
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#3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-BEN / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4% SODIUM CHLORIDE, 100MM SODIUM ACETATE PH 4.6, 120MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 14274 / % possible obs: 92.4 % / Redundancy: 2.99 % / CC1/2: 0.869 / Rmerge(I) obs: 0.36 / Net I/σ(I): 2.34 |
Reflection shell | Resolution: 2→2.12 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 2226 / CC1/2: 0.145 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4N8Z Resolution: 2→39.65 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.438 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.591 Å2
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Refinement step | Cycle: 1 / Resolution: 2→39.65 Å
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Refine LS restraints |
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