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Open data
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Basic information
Entry | Database: PDB / ID: 6y0e | ||||||
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Title | Nbe LBM | ||||||
![]() | NBe-LBM | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | TERBIUM(III) ION![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | ||||||
![]() | ![]() Title: Engineered nanobodies with a lanthanide binding motif for crystallographic phasing Authors: Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.4 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
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14862.208 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NBe-LBM / Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.54 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30 %(w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50.61 Å / Num. obs: 34335 / % possible obs: 99.3 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 22.1 / Num. measured all: 443937 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.78 Å2 / Biso mean: 22.398 Å2 / Biso min: 8.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→46.764 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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