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Open data
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Basic information
Entry | Database: PDB / ID: 1i3v | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF A LAMA VHH DOMAIN UNLIGANDED | ||||||
![]() | ANTIBODY VHH LAMA DOMAIN | ||||||
![]() | IMMUNE SYSTEM / antibody / domain VHH / Lama | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Spinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, C. | ||||||
![]() | ![]() Title: Lateral recognition of a dye hapten by a llama VHH domain. Authors: Spinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, 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 | ![]() | 63.6 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 439 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i3uSC 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 14049.452 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG MME 5000, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 42 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→25 Å / Num. all: 57618 / Num. obs: 16273 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.046 |
Reflection shell | Resolution: 2.01→2.12 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4 / Num. unique all: 2005 / Rsym value: 0.169 / % possible all: 94.6 |
Reflection | *PLUS Num. measured all: 57618 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 4.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1I3U Resolution: 2.03→14.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1727957.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.72 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→14.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 0 / Rfactor obs: 0.211 / Rfactor Rfree: 0.244 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.345 / % reflection Rfree: 7 % / Rfactor Rwork: 0.272 |