[English] 日本語
![](img/lk-miru.gif)
- PDB-5kvj: Crystal structure of the 16-mer doublestranded RNA. Northeast Str... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kvj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the 16-mer doublestranded RNA. Northeast Structural Genomics Consortium (NESG) target RNA1 | ||||||
![]() |
| ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Ma, L.-C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the 16-mer double stranded RNA. Authors: Vorobiev, S.M. / Ma, L.-C. / Montelione, G.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3nd3S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 5033.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: RNA chain | Mass: 5193.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-ARG / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: microbatch under paraffin oil / pH: 9 Details: 2.4 M Ammonium sulfate, 0.1 M BICINE, pH 9.0, dsRNA buffer: 0.025M NH4OAc, pH 5.5, 0.275 M NaCl, 0.005 M CaCl2, 0.001 M EDTA, 0.001 M TCEP, 0.025 M Arg, and 0.02% NaN3 PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.26→50 Å / Num. obs: 3824 / % possible obs: 93.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 3nd3 Resolution: 2.261→21.649 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.14
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.261→21.649 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2605→21.6505 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|