+Open data
-Basic information
Entry | Database: PDB / ID: 4jo4 | ||||||
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Title | Crystal structure of rabbit mAb R20 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Pan, R.M. / Kong, X.P. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans. Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jo4.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jo4.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/4jo4 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/4jo4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22596.881 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23888.824 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / Keywords: Fab #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.03 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4 M ammonium sulfate, 1.7% PEG400, 85 mM HEPES, pH 7.5, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2012 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→38.27 Å / Num. all: 53673 / Num. obs: 53548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.175 / Rsym value: 0.107 / Net I/σ(I): 22.55 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.105 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.593 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→38.268 Å / SU ML: 0.32 / σ(F): 0.23 / Phase error: 22.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.892 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.27→38.268 Å
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Refine LS restraints |
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LS refinement shell |
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