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- PDB-7ot7: sTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ot7 | |||||||||
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Title | sTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 2) | |||||||||
![]() | sTIM11noCys-SB | |||||||||
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Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Romero-Romero, S. / Kordes, S. / Hocker, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels. Authors: Kordes, S. / Romero-Romero, S. / Lutz, L. / Hocker, B. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.8 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7osuC ![]() 7osvC ![]() 7ot8C ![]() 7p12C ![]() 5bvlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22977.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: M (N-terminal) and GLEHHHHHH (C-terminal) come from the expresion vector. Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b(+) / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.8 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 34% PEG 400, 0.1 M Tris pH7.78, 0.2 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.51→47.33 Å / Num. obs: 27801 / % possible obs: 99.87 % / Redundancy: 13.8 % / Biso Wilson estimate: 28.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0596 / Rpim(I) all: 0.017 / Rrim(I) all: 0.0619 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.51→1.57 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2677 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.683 / Rrim(I) all: 2.35 / % possible all: 99.04 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5bvl Resolution: 1.51→47.33 Å / SU ML: 0.2068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0311 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: 40.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→47.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.7751386333 Å / Origin y: 7.57193852469 Å / Origin z: 4.94351960703 Å
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Refinement TLS group | Selection details: all |