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Open data
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Basic information
Entry | Database: PDB / ID: 5i1i | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-53/IGKV4-1 | ||||||
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![]() | IMMUNE SYSTEM / MONOCLONAL ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teplyakov, A. / Obmolova, G. / Malia, T. / Luo, J. / Gilliland, G. | ||||||
![]() | ![]() Title: Structural diversity in a human antibody germline library. Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Muzammil, S. / Sweet, R. / Almagro, J.C. / Gilliland, G.L. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Protein crystallization with microseed matrix screening: application to human germline antibody Fabs. Authors: Obmolova, G. / Malia, T.J. / Teplyakov, A. / Sweet, R.W. / Gilliland, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i15C ![]() 5i16C ![]() 5i17C ![]() 5i18C ![]() 5i19C ![]() 5i1aC ![]() 5i1cC ![]() 5i1dSC ![]() 5i1eC ![]() 5i1gC ![]() 5i1hC ![]() 5i1jC ![]() 5i1kC ![]() 5i1lC C: citing same article ( S: Starting model for refinement |
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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
#1: Antibody | Mass: 24229.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 24239.059 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: 2.64 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES PH 6.5, 17% PEG 3K, 0.2 M SODIUM FORMATE, 5% MPD PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 24, 2008 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 16727 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 5.6 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I1D Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.85 / SU B: 15.401 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.689 / ESU R Free: 0.392
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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