[English] 日本語
Yorodumi- PDB-6ual: A Self-Assembling DNA Crystal Scaffold with Cavities Containing 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ual | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A Self-Assembling DNA Crystal Scaffold with Cavities Containing 3 Helical Turns per Edge | |||||||||
Components |
| |||||||||
Keywords | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice | |||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.514 Å | |||||||||
Authors | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To Be Published Title: Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry Authors: Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ual.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ual.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ual.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ual_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ual_full_validation.pdf.gz | 382.7 KB | Display | |
Data in XML | 6ual_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 6ual_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/6ual ftp://data.pdbj.org/pub/pdb/validation_reports/ua/6ual | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 9718.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 6207.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 7.6 Å3/Da / Density % sol: 83.81 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M cacodylate pH 7.0, 20 mM MgCl2, 1mM spermine, 1.0 mM cobalt hexamine, 15% ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock. Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.514→50 Å / Num. obs: 3195 / % possible obs: 95.1 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.034 / Rrim(I) all: 0.104 / Χ2: 4.623 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.514→45.978 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 35.03
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 589.29 Å2 / Biso min: 112.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.514→45.978 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 4.5141→45.9805 Å / Rfactor Rfree error: 0
|