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Yorodumi- PDB-7o53: Structure of thaumatin determined at SwissFEL using native-SAD at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o53 | ||||||
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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 XGANDALF with 50000 indexed images | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / thaumatin / SwissFEL / native-SAD / SASE / large bandwidth / pink | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 2.2 Å | ||||||
Authors | Nass, K. | ||||||
Citation | Journal: To Be Published Title: Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and XGANDALF with 50000 indexed images Authors: Nass, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o53.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o53.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 7o53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/7o53 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/7o53 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Experimental dataset #1 | Data reference: 10.11577/1814882 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 2.059 Å |
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: 2.2→24.8 Å / Num. obs: 25539 / % possible obs: 100 % / Redundancy: 206 % / Biso Wilson estimate: 48.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.25 Å / Mean I/σ(I) obs: 0.94 / Num. unique obs: 1738 / CC1/2: 0.424 / R split: 1.04 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→24.73 Å / SU ML: 0.2317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8145 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: 49.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.73 Å
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Refine LS restraints |
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LS refinement shell |
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