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Open data
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Basic information
Entry | Database: PDB / ID: 4krn | ||||||
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Title | Nanobody/VHH domain EgA1 | ||||||
![]() | Nanobody/VHH domain EgA1 | ||||||
![]() | IMMUNE SYSTEM / nanobody / VHH domain / Camelid VH domain / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ferguson, K.M. / Schmitz, K.R. | ||||||
![]() | ![]() Title: Structural Evaluation of EGFR Inhibition Mechanisms for Nanobodies/VHH Domains. Authors: Schmitz, K.R. / Bagchi, A. / Roovers, R.C. / van Bergen En Henegouwen, P.M. / Ferguson, K.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.3 KB | Display | ![]() |
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Full document | ![]() | 435.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4krlC ![]() 4krmC ![]() 4kroC ![]() 4krpC ![]() 1i3vS C: citing same article ( 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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Unit cell |
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Components
#1: Antibody | Mass: 15546.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG3350, 0.2 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→31.357 Å / Num. all: 24694 / Num. obs: 24694 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.037 / Χ2: 1.705 / Net I/σ(I): 19 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1I3V Resolution: 1.553→26.96 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.2094 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8697 / SU B: 2.404 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0875 / SU Rfree: 0.0768 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.16 Å2 / Biso mean: 21.8934 Å2 / Biso min: 13.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.553→26.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.553→1.593 Å / Total num. of bins used: 20
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