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Open data
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Basic information
Entry | Database: PDB / ID: 5m7q | ||||||
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Title | Engineering the Thermostability of Nanobodies - NbD2 | ||||||
![]() | Nanobody NbD2 | ||||||
![]() | IMMUNE SYSTEM / Nanobody / VHH / variable domain / Camelids | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soler, N. / Kunz, P. / Muyldermans, S. | ||||||
![]() | ![]() Title: Engineering the Thermostability of Nanobodies Authors: Kunz, P. / Flock, T. / Soler, N. / Zaiss, M. / Vincke, C. / Sterckx, Y. / Muyldermans, S. / Kastelic, D. / Hoheisel, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 48.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
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Full document | ![]() | 446.6 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4w6xS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15046.653 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, pH 6.5, 1.6 M magnesium sulfate heptahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.69 Å / Num. obs: 30508 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.775 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4W6X Resolution: 1.8→25.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.092 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.887 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→25.69 Å
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Refine LS restraints |
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