+Open data
-Basic information
Entry | Database: PDB / ID: 7mu4 | ||||||
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Title | Crystal Structure of HPV L1-directed D24.M01Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antigen Binding Fragment (Fab) | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Singh, S. / Pancera, M. | ||||||
Citation | Journal: To Be Published Title: Structural Characterisation of Immune Responses to HPV Vaccination Authors: Singh, S. / Pancera, M. / Rodarte, J. / Carter, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mu4.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mu4.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/7mu4 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/7mu4 | HTTPS FTP |
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-Related structure data
Related structure data | 7mx8C 6apbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 29735.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24920.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 6000, 5% v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→46.63 Å / Num. obs: 33966 / % possible obs: 89 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.83→1.9 Å / Num. unique obs: 1715 / CC1/2: 0.714 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6APB Resolution: 1.83→46.62 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2893 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: 28.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→46.62 Å
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Refine LS restraints |
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LS refinement shell |
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