+Open data
-Basic information
Entry | Database: PDB / ID: 8vrr | ||||||
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Title | 4H11-scFv antibody | ||||||
Components | 4H11 scFv chain | ||||||
Keywords | PEPTIDE BINDING PROTEIN / IMMUNE SYSTEM / Single-chain ANTIBODY Humanized Nanobody | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Lee, K. / Perry, K. / Yeku, O.O. / Spriggs, D.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Ovarian Res / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vrr.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vrr.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vrr_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 8vrr_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 8vrr_validation.xml.gz | 12 KB | Display | |
Data in CIF | 8vrr_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vrr ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vrr | HTTPS FTP |
-Related structure data
-Links
-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.) Mus musculus (house mouse) / Cell line (production host): HEK293T/17 / Production host: Homo sapiens (human) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→75.33 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.3573 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 |