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- PDB-6fj9: Structure of Thaumatin collected from an in situ crystal on ID30B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fj9 | ||||||
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Title | Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV. | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN | ||||||
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 | ![]() | 97.9 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fidC ![]() 6fj2C ![]() 6fj4C ![]() 6fj6C ![]() 6fj8C ![]() 5a47S 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % / Description: Bipyramidal crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES and 0.7 M potassium/sodium tartrate |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2016 Details: Be CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing) |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7085 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→54.63 Å / Num. obs: 39794 / % possible obs: 92.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1988 / CC1/2: 0.6 / Rpim(I) all: 0.518 / Rrim(I) all: 0.979 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5a47 Resolution: 1.5→54.63 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.533 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.775 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→54.63 Å
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Refine LS restraints |
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