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Open data
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Basic information
Entry | Database: PDB / ID: 1wt5 | ||||||
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Title | The Crystal Structure Of A Humanized Antibody Fv 528 | ||||||
![]() | (ANTI EGFR ANTIBODY FV REGION) x 2 | ||||||
![]() | IMMUNE SYSTEM / HUMANIZED ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Makabe, K. / Tsumoto, K. / Asano, R. / Kondo, H. / Kumagai, I. | ||||||
![]() | ![]() Title: Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528 Authors: Makabe, K. / Nakanishi, T. / Tsumoto, K. / Tanaka, Y. / Kondo, H. / Umetsu, M. / Sone, Y. / Asano, R. / Kumagai, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 79.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 14162.790 Da / Num. of mol.: 2 / Fragment: VH fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 13464.060 Da / Num. of mol.: 2 / Fragment: VL fragment 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: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: NaCl, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.0695→49.3865 Å / Num. all: 30360 / Num. obs: 30360 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.061 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4392 / Rsym value: 0.186 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.5896 Å2 / ksol: 0.371454 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |