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- PDB-6ybx: RT structure of Thaumatin obtained at 1.14 A resolution from crys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ybx | ||||||
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Title | RT structure of Thaumatin obtained at 1.14 A resolution from crystal grown in a Mylar microchip. | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN / SWEET TASTING PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gavira, J.A. / Martinez-Rodriguez, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.4 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ybfC ![]() 6ybiC ![]() 6yboC ![]() 6ybrC ![]() 6yc5C ![]() 1thwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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 natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-TLA / |
#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: 2.9 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293.5 K / Method: counter-diffusion / pH: 7 / Details: 20% w/v NaK Tartrate / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017 Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→46.34 Å / Num. obs: 89815 / % possible obs: 92.35 % / Redundancy: 31.69 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.14→1.18 Å / Num. unique obs: 5094 / CC1/2: 0.791 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1THW Resolution: 1.14→46.34 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4692 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: 22.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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