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Open data
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Basic information
Entry | Database: PDB / ID: 6mnf | ||||||||||||
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Title | Anti-HIV-1 Fab 2G12 + Man8 re-refinement | ||||||||||||
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![]() | IMMUNE SYSTEM / HIV-1 carbohydrate broadly neutralizing antibody / hiv neutralizing antibody / anti-carbohydrate / domain-swapping | ||||||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Calarese, D.A. / Stanfield, R.L. / Wilson, I.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Authors: Calarese, D.A. / Lee, H.K. / Huang, C.Y. / Best, M.D. / Astronomo, R.D. / Stanfield, R.L. / Katinger, H. / Burton, D.R. / Wong, C.H. / Wilson, I.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.6 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 844.5 KB | Display | ![]() |
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Full document | ![]() | 851.8 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6msyC ![]() 6mu3C ![]() 6mubC ![]() 1op3 S: Starting model for refinement C: citing same article ( |
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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: 23245.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 23845.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 4000, 0.2M imidazole malate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 33657 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.929 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 1675 / Χ2: 0.823 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OP3 ![]() 1op3 Resolution: 2.758→41.071 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.758→41.071 Å
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Refine LS restraints |
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LS refinement shell |
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