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Open data
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Basic information
Entry | Database: PDB / ID: 3ds7 | ||||||
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Title | Structure of an RNA-2'-deoxyguanosine complex | ||||||
![]() | 67-MER | ||||||
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Function / homology | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Edwards, A.L. / Batey, R.T. | ||||||
![]() | ![]() Title: A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. Authors: Edwards, A.L. / Batey, R.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 | ![]() | 104.1 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1u8d 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 21542.873 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence is synthetic derived from a mutagenesis study #2: Chemical | ![]() #3: Chemical | ChemComp-NCO / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.01M K-HEPES, 0.0119 M cobalt(III) hexammine, 22% PEG 2000, 0.66M ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 12, 2007 |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→19.5 Å / Num. all: 31039 / Num. obs: 29177 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 3.56 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2822 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB 1U8D ![]() 1u8d Resolution: 1.85→19.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 518064.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.7773 Å2 / ksol: 0.45 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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