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- PDB-3q6g: Crystal structure of Fab of rhesus mAb 2.5B specific for quaterna... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q6g | ||||||
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Title | Crystal structure of Fab of rhesus mAb 2.5B specific for quaternary neutralizing epitope of HIV-1 gp120 | ||||||
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![]() | IMMUNE SYSTEM / Ig / neutralization of HIV-1 viruses / Quaternary epitope of HIV-1 gp120 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spurrier, B. / Sampson, J. / Totrov, M. / Li, H. / O'Neal, T. / William, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P. | ||||||
![]() | ![]() Title: Structural Analysis of Human and Macaque mAbs 2909 and 2.5B: Implications for the Configuration of the Quaternary Neutralizing Epitope of HIV-1 gp120. Authors: Spurrier, B. / Sampson, J.M. / Totrov, M. / Li, H. / O'Neal, T. / Williams, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.9 KB | Display | ![]() |
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PDB format | ![]() | 155.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 461.5 KB | Display | |
Data in XML | ![]() | 42.5 KB | Display | |
Data in CIF | ![]() | 62.6 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 22180.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Antibody | Mass: 24780.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 18% PEG 3350, 100 mM ammonium nitrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2009 / Details: Mirrors | |||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 68825 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.85 / Net I/σ(I): 17.8 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.299 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.902→29.702 Å
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Refine LS restraints |
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LS refinement shell |
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