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- PDB-2axj: Crystal structures of T cell receptor beta chains related to rheu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2axj | ||||||
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Title | Crystal structures of T cell receptor beta chains related to rheumatoid arthritis | ||||||
![]() | SF4 T cell receptor beta chain | ||||||
![]() | IMMUNE SYSTEM / TCR | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y. | ||||||
![]() | ![]() Title: Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis. Authors: Li, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 85.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.5 KB | Display | ![]() |
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Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2axhSC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27531.547 Da / Num. of mol.: 2 / Fragment: extracellular domain 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: 3.95 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.6-0.7 M sodium citrate, 0.1 M HEPES, 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: Oct 18, 2002 |
Radiation | Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 26667 / Num. obs: 25627 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 1.165 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.65→2.74 Å / % possible obs: 77.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 2012 / Num. unique all: 2012 / Rsym value: 0.614 / Χ2: 0.954 / % possible all: 77.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AXH Resolution: 2.65→41.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2985620 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.659 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→41.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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