[English] 日本語
![](img/lk-miru.gif)
- PDB-6rnf: Liquid Application Method for time-resolved Analyses (LAMA) by se... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rnf | ||||||
---|---|---|---|---|---|---|---|
Title | Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 30 ms 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qnbC ![]() 6qncC ![]() 6qndC ![]() 6qnhC ![]() 6qniC ![]() 6qnjC ![]() 6rnbC ![]() 6rncC ![]() 6rndC ![]() 3kbnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-GLC / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.699→65.72 Å / Num. obs: 45700 / % possible obs: 99.99 % / Redundancy: 435.3 % / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.699→1.73 Å / Num. unique obs: 4499 |
Serial crystallography sample delivery | Method: fixed target |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3KBN Resolution: 1.7→65.72 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→65.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|