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Open data
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Basic information
Entry | Database: PDB / ID: 8vrr | ||||||
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Title | 4H11-scFv antibody | ||||||
![]() | 4H11 scFv chain | ||||||
![]() | PEPTIDE BINDING PROTEIN / IMMUNE SYSTEM / Single-chain ANTIBODY Humanized Nanobody | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, K. / Perry, K. / Yeku, O.O. / Spriggs, D.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for antibody recognition of the proximal MUC16 ectodomain. Authors: Lee, K. / Perry, K. / Xu, M. / Veillard, I. / Kumar, R. / Rao, T.D. / Rueda, B.R. / Spriggs, D.R. / Yeku, O.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.8 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.3 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 27449.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Anti-CD34 Monoclonal Antibody scFv fragment / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Sodium Citrate, pH 5.0, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 183 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020 / Details: KB Focussing Mirrors |
Radiation | Monochromator: Single Crystal Si-220 Side-Bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→90.3 Å / Num. obs: 18408 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Χ2: 0.97 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.36→2.45 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.688 / Num. unique obs: 1817 / CC1/2: 0.622 / Rpim(I) all: 1.098 / Rrim(I) all: 2.021 / Χ2: 0.74 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→75.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.43290532757 Å / Origin y: 8.85744670286 Å / Origin z: -21.8763102756 Å
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Refinement TLS group | Selection details: all |