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- PDB-7cdr: Lysozyme room-temperature structure determined by SS-ROX combined... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cdr | |||||||||
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Title | Lysozyme room-temperature structure determined by SS-ROX combined with HAG method, 210 kGy (3000 images) | |||||||||
![]() | Lysozyme C | |||||||||
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Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method. Authors: Hasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.2 KB | Display | ![]() |
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PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cdkC ![]() 7cdmC ![]() 7cdnC ![]() 7cdoC ![]() 7cdpC ![]() 7cdqC ![]() 7cdsC ![]() 7cdtC ![]() 7cduC ![]() 4etaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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-MLI / ![]() |
#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: 40.64 % |
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Crystal grow![]() | Temperature: 293 K / Method: batch mode Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was ...Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was stopped by adding 2.4 M Na-Malonate pH 3.1, 3.6 % w/v PEG6000. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→55.42 Å / Num. obs: 11698 / % possible obs: 100 % / Redundancy: 182.7 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.9711 / Net I/σ(I): 5.67 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 579 / CC1/2: 0.6723 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4eta Resolution: 1.8→55.42 Å / SU ML: 0.1715 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8367 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: 14.18 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→55.42 Å
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Refine LS restraints |
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LS refinement shell |
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