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Open data
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Basic information
Entry | Database: PDB / ID: 6fj6 | ||||||
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Title | Structure of Thaumatin collected at 100K on ID30B | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN / Sweet protein from Thaumatococcus daniellii | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McCarthy, A.A. / Mueller-Dieckmann, C. | ||||||
![]() | ![]() Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, 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 | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fidC ![]() 6fj2C ![]() 6fj4C ![]() 6fj8C ![]() 6fj9C ![]() 3e0aS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
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: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % / Description: Large bipyramids |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 0.7 M sodium/potassium tartrate and 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2017 Details: Be CRL (vertical focusing) and Rh coating elliptical mirror (horizontal focusing) |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→54.09 Å / Num. obs: 99222 / % possible obs: 89.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.029 / Rrim(I) all: 0.069 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.08→1.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6841 / CC1/2: 0.857 / Rpim(I) all: 0.544 / Rrim(I) all: 0.845 / % possible all: 63.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3e0a Resolution: 1.08→54.09 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.069 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.711 Å2
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Refinement step | Cycle: 1 / Resolution: 1.08→54.09 Å
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Refine LS restraints |
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