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- PDB-6xrq: Structural descriptions of ligand interactions to DNA and RNA qua... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xrq | ||||||||||||||||||||
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Title | Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus | ||||||||||||||||||||
![]() | RNA (5' GP*![]() RNA / Quadruplex / PRV | Function / homology | : / Chem-V8A / RNA / RNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() ![]() Zhang, Y.S. / Parkinson, G.N. / Wei, D.G. | ![]() ![]() Title: Structural descriptions of ligand interactions to RNA quadruplexes folded from the non-coding region of Pseudorabies virus. Authors: Zhang, Y. / Bux, K. / Attana, F. / Wei, D. / Haider, S. / Parkinson, G.N. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.8 KB | Display | ![]() |
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PDB format | ![]() | 23.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jjhS 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: RNA chain | Mass: 4572.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() Absorpt process details: CCP4 7.0.075: AIMLESS, version 0.7.4 : 13/12/18 Scaling & analysis of unmerged intensities, absorption correction using spherical harmonics Number of used crystals: 1 |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.97 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Potassium cacodylate, Potassium chloride, Sodium cacodylate, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2019 | ||||||||||||||||||||||||
Radiation | Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Limit h max: 20 / Limit h min: -21 / Limit k max: 28 / Limit k min: -29 / Limit l max: 23 / Limit l min: -21 / Number: 47094 / Theta max: 23.6140252043 ° / Theta min: 0.934183571367 ° | ||||||||||||||||||||||||
Reflection | Resolution: 1.21→27.703 Å / Num. obs: 21248 / % possible obs: 94.1 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Cell measurement | Reflection used: 47094 / Theta max: 23.6140252043 ° / Theta min: 0.934183571367 ° |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JJH Resolution: 1.21→27.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.926 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.056 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.82 Å2
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Refinement step | Cycle: final / Resolution: 1.21→27.69 Å
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Refine LS restraints |
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LS refinement shell |
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