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- PDB-6was: Structure of D19.PA8 Fab in complex with 1FD6 16055 V1V2 scaffold -
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Open data
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Basic information
Entry | Database: PDB / ID: 6was | |||||||||
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Title | Structure of D19.PA8 Fab in complex with 1FD6 16055 V1V2 scaffold | |||||||||
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![]() | IMMUNE SYSTEM / Fragment binding antigen and peptide complex | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singh, S. / Liban, T.J. / Pancera, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 378.4 KB | Display | ![]() |
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PDB format | ![]() | 305.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vjnC ![]() 6witC ![]() 6xlzC ![]() 6xsnC ![]() 5tdnS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23814.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23409.592 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 17102.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 18% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 1, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 84549 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.991 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 1342 / CC1/2: 0.563 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDb entry 5TDN Resolution: 1.904→31.903 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.09 Å2 / Biso mean: 32.4123 Å2 / Biso min: 6.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.904→31.903 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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