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- PDB-5aq7: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aq7 | |||||||||
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Title | DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography | |||||||||
![]() | D12_DB04V3 | |||||||||
![]() | 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 / MALONATE 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 | ![]() | 459.1 KB | Display | ![]() |
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PDB format | ![]() | 388.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5aq8C ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45205.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PEG3350 20.0% W/V, SODIUM MALONATE 0.2 M, BIS TRIS PROPANE 0.1M, 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: Apr 3, 2012 / 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: 2.1→43.49 Å / Num. obs: 50274 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.59 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.36 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A Resolution: 2.1→43.488 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 25.82 / 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: 50.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.488 Å
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Refine LS restraints |
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LS refinement shell |
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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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