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- PDB-4x4z: Retrofitting antibodies with stabilizing mutations. Herceptin VL ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x4z | ||||||
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Title | Retrofitting antibodies with stabilizing mutations. Herceptin VL mutant F53D. | ||||||
![]() | Herceptin VL domain with F53D mutation | ||||||
![]() | IMMUNE SYSTEM / antibody stabilization mutations | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Langley, D.B. / Rouet, R. / Christ, D. | ||||||
![]() | ![]() Title: Retrofitting antibodies with stabilizing mutations Authors: Langley, D.B. / Rouet, R. / 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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.1 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 13.7 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 on special symmetry positions |
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Components
#1: Antibody | Mass: 11673.924 Da / Num. of mol.: 2 / Mutation: F53D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: square pyramidal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M Sodium Malonate, 100 mM HEPES (pH 7.0), 1% (v/v) Jeffamine ED-2003 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.77 Å / Num. obs: 26083 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
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Processing
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Refinement | Resolution: 1.8→37.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.001 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / 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: 24.19 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→37.77 Å
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Refine LS restraints |
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