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- PDB-4x4x: Retrofitting antibodies with stabilizing mutations. Herceptin scF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x4x | ||||||
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Title | Retrofitting antibodies with stabilizing mutations. Herceptin scFv mutant. | ||||||
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![]() | IMMUNE SYSTEM / antibody stabilization mutations | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Langley, D.B. / Roome, B. / Christ, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Retrofitting antibodies with stabilizing mutations Authors: Langley, D.B. / Roome, B. / Christ, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.1 KB | Display | ![]() |
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PDB format | ![]() | 138.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 22.4 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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Unit cell |
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Components
#1: Antibody | Mass: 14565.989 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 11734.021 Da / Num. of mol.: 2 / Mutation: S52D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: small hexagonal rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 3.5 M sodium formate, 100 mM sodium acetate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→35.65 Å / Num. obs: 26621 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Resolution: 2.25→35.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.039 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.337 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→35.65 Å
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Refine LS restraints |
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