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Open data
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Basic information
Entry | Database: PDB / ID: 6xyf | ||||||
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Title | Nanobody 22 | ||||||
![]() | Nanobody 22 | ||||||
![]() | IMMUNE SYSTEM / Nanobody | ||||||
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 | ![]() | 96 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 419 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xymC ![]() 6xzfC ![]() 6y0eC ![]() 6y1rC ![]() 4i13S 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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Unit cell |
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Components
#1: Antibody | Mass: 14276.796 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis Tris Propane 100 mM Na/K Phosphate 30 % PEG 3350 |
-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: May 30, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9484 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.11→30.01 Å / Num. obs: 39057 / % possible obs: 96.3 % / Redundancy: 12.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.037 / Rrim(I) all: 0.135 / Net I/σ(I): 10.2 / Num. measured all: 495655 / Scaling rejects: 668 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4i13.pdb Resolution: 1.11097→30.0062 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 13.7 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11097→30.0062 Å
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Refine LS restraints |
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