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Open data
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Basic information
Entry | Database: PDB / ID: 4yhn | ||||||
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Title | Dabigatran Reversal Agent | ||||||
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![]() | IMMUNE SYSTEM / antibodies | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schiele, F. / Nar, H. | ||||||
![]() | ![]() Title: Structure-guided residence time optimization of a dabigatran reversal agent. Authors: Schiele, F. / van Ryn, J. / Litzenburger, T. / Ritter, M. / Seeliger, D. / Nar, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.8 KB | Display | ![]() |
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PDB format | ![]() | 285 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ygvC ![]() 4yhiC ![]() 4yhkC ![]() 4yhlC ![]() 4yhmC ![]() 4yhoC ![]() 1c1eS 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
#1: Antibody | Mass: 23767.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24116.936 Da / Num. of mol.: 2 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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM PCB buffer (pH 6) and 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→29.98 Å / Num. obs: 33587 / % possible obs: 89.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 39.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.31→2.81 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C1E Resolution: 2.31→21.22 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.8782 / SU R Cruickshank DPI: 0.497 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.467 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.242
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Displacement parameters | Biso mean: 37.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.284 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.31→21.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.38 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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