[English] 日本語
Yorodumi- PDB-6g89: Thaumatin solved by Native SAD from a dataset collected in 0.6 se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g89 | ||||||
---|---|---|---|---|---|---|---|
Title | Thaumatin solved by Native SAD from a dataset collected in 0.6 second with JUNGFRAU detector | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / Native-SAD / JUNGFRAU / integrating detector | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.359 Å | ||||||
Authors | Leonarski, F. / Olieric, V. / Vera, L. / Redford, S. / Wang, M. | ||||||
Citation | Journal: Nat. Methods / Year: 2018 Title: Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector. Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / ...Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / Diederichs, K. / Bunk, O. / Schmitt, B. / Wang, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g89.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g89.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g89 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g89 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22156.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% Sodium Potassium Tartrate, 100 mM Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 2.0667 Å |
Detector | Type: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jul 16, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0667 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→37.813 Å / Num. obs: 16463 / % possible obs: 82.3 % / Redundancy: 2.1 % / Rrim(I) all: 0.035 / Net I/σ(I): 23.35 |
Reflection shell | Resolution: 2.36→2.5 Å / Mean I/σ(I) obs: 9.65 / Num. unique obs: 923 / Rrim(I) all: 0.065 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.359→37.813 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.14 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.359→37.813 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|