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- PDB-6qnd: Liquid Application Method for time-resolved Analyses (LAMA) by se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qnd | ||||||
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Title | Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 60 s timepoint | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / Complex / Diffusion / Dynamics | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mehrabi, P. / Schulz, E.C. / Miller, R.J.D. | ||||||
![]() | ![]() Title: Liquid application method for time-resolved analyses by serial synchrotron crystallography. Authors: Mehrabi, P. / Schulz, E.C. / Agthe, M. / Horrell, S. / Bourenkov, G. / von Stetten, D. / Leimkohl, J.P. / Schikora, H. / Schneider, T.R. / Pearson, A.R. / Tellkamp, F. / Miller, R.J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.3 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qnbC ![]() 6qncC ![]() 6qnhC ![]() 6qniC ![]() 6qnjC ![]() 6rnbC ![]() 6rncC ![]() 6rndC ![]() 6rnfC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Sugar | ChemComp-GLO / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→20.055 Å / Num. obs: 28312 / % possible obs: 99.64 % / Redundancy: 54.8 % / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2→2.07 Å |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Resolution: 2.001→20.055 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→20.055 Å
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Refine LS restraints |
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LS refinement shell |
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