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Open data
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Basic information
Entry | Database: PDB / ID: 6tkd | ||||||
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Title | ChiLob 7/4 H2 HC-C228S F(ab')2 | ||||||
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Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orr, C.M. / Fisher, H. / Tews, I. | ||||||
![]() | ![]() Title: Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility. Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A. ...Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A.L. / Essex, J.W. / Pearson, A.R. / Cragg, M.S. / Tews, 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 | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tkbC ![]() 6tkcC ![]() 6tkeC ![]() 6tkfC ![]() 6faxS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 25099.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23463.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.64 % / Description: needle |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→128.19 Å / Num. obs: 45431 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→1.94 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2857 / CC1/2: 0.768 / Rpim(I) all: 0.32 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6FAX Resolution: 1.9→128.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.174 / Average fsc free: 0.9341 / Average fsc work: 0.9457 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.12 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.549 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→128.19 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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