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- PDB-5aq8: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aq8 | ||||||
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Title | DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography | ||||||
![]() | OFF7_DB12V4 | ||||||
![]() | CHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION | ||||||
Function / homology | Ankyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / THIOCYANATE ION![]() | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A. | ||||||
![]() | ![]() Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.9 KB | Display | ![]() |
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PDB format | ![]() | 198.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.7 KB | Display | ![]() |
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Full document | ![]() | 446.5 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aq7C ![]() 5aq9C ![]() 5aqaC ![]() 5aqbC ![]() 1svxS ![]() 3dtmS 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: Protein | Mass: 45962.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PEG4000 18.3 %, KSCN 0.286 M, HEPES-NA, 0.1 M, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR |
Radiation | Monochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→43.72 Å / Num. obs: 43423 / % possible obs: 1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.13 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.51 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A Resolution: 1.62→43.717 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 26.86 / 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 mean: 26.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→43.717 Å
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Refine LS restraints |
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LS refinement shell |
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