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Open data
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Basic information
Entry | Database: PDB / ID: 7dfy | |||||||||
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Title | Novel motif for left-handed G-quadruplex formation | |||||||||
![]() | 2xMotif2 | |||||||||
![]() | DNA / Left-handed / G-quadruplex / Bulge / four-layer | |||||||||
Function / homology | : / STRONTIUM ION / DNA / DNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Das, P. / Winnerdy, F.R. / Maity, A. / Mechulam, Y. / Phan, A.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A novel minimal motif for left-handed G-quadruplex formation. Authors: Das, P. / Winnerdy, F.R. / Maity, A. / Mechulam, Y. / Phan, A.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.5 KB | Display | ![]() |
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Full document | ![]() | 399.5 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gz6S 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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Unit cell |
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Components
#1: DNA chain | Mass: 8264.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA motif for left-handed G-quadruplex formation / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-SR / #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.08 M Strontium Chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate ph=6.0, 35% v/v (+/-)-2-Methyl-2,4-pentanediol (MPD), 0.012 M Spermine tetrahydrochoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→76.995 Å / Num. obs: 9010 / % possible obs: 86.2 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.08 / Rrim(I) all: 0.206 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.69→1.904 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1 / Num. unique obs: 450 / CC1/2: 0.349 / Rpim(I) all: 0.739 / % possible all: 40.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6gz6 Resolution: 1.69→76.99 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.48 / 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 max: 115.53 Å2 / Biso mean: 21.7197 Å2 / Biso min: 0.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→76.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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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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