[English] 日本語
Yorodumi- PDB-7at6: Structure of thaumatin collected by femtosecond serial crystallog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7at6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of thaumatin collected by femtosecond serial crystallography on a COC membrane | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Martiel, I. / Marsh, M. / Vera, L. / Huang, C.Y. / Olieric, V. / Leonarski, P. / Nass, K. / Padeste, C. / Karpik, A. / Wang, M. / Pedrini, B. | ||||||
Citation | Journal: To Be Published Title: Commissioning results from the SwissMX instrument for fixed target macromolecular crystallography at SwissFEL Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, ...Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, C. / Karpik, A. / Thominet, V. / Hora, J. / Olieric, N. / Weinert, T. / Wranik, M. / Brunle, S. / Standfuss, J. / Aurelius, O. / John, J. / Hogbom, M. / Zhang, L. / Einsle, O. / Papp, G. / Basu, S. / Cipriani, F. / Beaud, P. / Mankowsky, R. / Glettig, W. / Mozzanica, A. / Redford, S. / Schmidt, B. / Bunk, O. / Abela, R. / Wang, M. / Lemke, H. / Pedrini, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7at6.cif.gz | 103 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7at6.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 7at6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7at6 ftp://data.pdbj.org/pub/pdb/validation_reports/at/7at6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7betC 4axrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22228.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02883 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PGR / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch mode Details: 1.6 M potassium sodium tartrate tetrahydrate 100mM Na Hepes pH 7.0 buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESB / Wavelength: 1.368 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Nov 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.368 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→36.353 Å / Num. obs: 46820 / % possible obs: 100 % / Redundancy: 530 % / CC1/2: 0.992 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.46→1.49 Å / Num. unique obs: 4574 / CC1/2: 0.306 |
Serial crystallography measurement | Pulse photon energy: 9.06 keV |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: SwissMX CM / Sample dehydration prevention: cryogenic conditions / Sample holding: COC membrane / Support base: SwissMX goniometer |
Serial crystallography data reduction | Frames indexed: 31000 / XFEL pulse events: 174400 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AXR Resolution: 1.46→36.353 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.37 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.12 Å2 / Biso mean: 37.0631 Å2 / Biso min: 26.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.46→36.353 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 12.35 Å / Origin y: 24.089 Å / Origin z: 32.606 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|