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Open data
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Basic information
Entry | Database: PDB / ID: 8ezx | |||||||||
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Title | Lysozyme Anomalous Dataset at 293 K and 7.1 keV | |||||||||
![]() | 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 | ![]() ![]() ![]() | |||||||||
![]() | Doukov, T. / Yabukarski, F. / Herschlag, D. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. Authors: Doukov, T. / Herschlag, D. / Yabukarski, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ezoC ![]() 8ezpC ![]() 8ezuC ![]() 8f00C ![]() 8f01C ![]() 8f03C ![]() 8f05C ![]() 8f06C ![]() 8f07C ![]() 8f0bC 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
#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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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5 uL of 0.6 M Sodium Chloride in 100 mM Sodium Acetate buffer pH 4.5 and 25% ethylene glycol were mixed with 5 uL 100 mg/mL lysozyme in 100 mM Sodium Acetate. |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7462 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.883 Å / Num. obs: 8682 / % possible obs: 92.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.022 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 5 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 2347 / CC1/2: 0.984 / Rpim(I) all: 0.084 / % possible all: 78.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.922 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.883 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.992 Å / Origin y: 40.289 Å / Origin z: -0.46 Å
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Refinement TLS group | Selection: ALL |