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- PDB-7o5j: Structure of thaumatin determined at SwissFEL using native-SAD at... -
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Basic information
Entry | Database: PDB / ID: 7o5j | ||||||
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Title | Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN / native-SAD / large bandwidth / pink beam / XFEL / SFX / serial crystallography | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nass, K. | ||||||
![]() | ![]() Title: Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer Authors: Nass, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 434.4 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Experimental dataset #1 | Data reference: ![]() |
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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: 22227.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7 Details: 1.6 M potassium sodium tartrate tetrahydrate, 100 mM Na-HEPES |
-Data collection
Diffraction | Mean temperature: 297 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.059 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→23.14 Å / Num. obs: 31565 / % possible obs: 100 % / Redundancy: 1218 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.999 / R split: 0.0243 / Net I/σ(I): 23.12 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 30 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2114 / CC1/2: 0.426 / R split: 1.006 / % possible all: 0.998 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() 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: 47.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→23.14 Å
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Refine LS restraints |
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LS refinement shell |
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