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Open data
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Basic information
Entry | Database: PDB / ID: 8dy3 | ||||||
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Title | Crystal Structure of spFv GLK2 HL | ||||||
![]() | spFv GLK2 HL | ||||||
![]() | IMMUNE SYSTEM / scFv / stapled scFv / spFv / germline scFv / single chain Fv / scFv stabilizations / antibody | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Crystal Structure of spFv GLK1 in LH configuration | ||||||
![]() | Luo, J. / Boucher, L.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: "Stapling" scFv for multispecific biotherapeutics of superior properties. Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / ...Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / Heyne, S. / Mazzanti, N. / Testa, J. / Diem, M.D. / Gorre, E. / Mahan, A. / Nanda, H. / Gunawardena, H.P. / Gervais, A. / Armstrong, A.A. / Teplyakov, A. / Huang, C. / Zwolak, A. / Chowdhury, P. / Cheung, W.C. / Luo, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.5 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.2 KB | Display | ![]() |
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Full document | ![]() | 429.8 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dy0C ![]() 8dy1C ![]() 8dy2C ![]() 8dy4C ![]() 8dy5C ![]() 3na9S S: Starting model for refinement C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 26647.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.5 / Details: 100 mM Na Acetate, 750 mM (NH4)2 SO4 |
-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: Apr 17, 2018 / Details: mirrors |
Radiation | Monochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.509→56.276 Å / Num. obs: 30532 / % possible obs: 94.2 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.509→1.654 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.678 / Num. unique obs: 1527 / CC1/2: 0.513 / Rpim(I) all: 0.568 / Rrim(I) all: 1.777 / % possible all: 68.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3na9 Resolution: 1.509→56.276 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.35 Å2 / Biso mean: 24.2488 Å2 / Biso min: 11.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.509→56.276 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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