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Open data
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Basic information
Entry | Database: PDB / ID: 2xc6 | |||||||||
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Title | Crystal structure of the GNA 3'-CTC(Br)UAGAG-2' | |||||||||
![]() | GNA | |||||||||
![]() | RNA / WATSON-CRICK BASE PAIR / GLYCOL NUCLEIC ACID | |||||||||
Function / homology | RNA![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schlegel, M.K. / Essen, L.-O. / Meggers, E. | |||||||||
![]() | ![]() Title: On the Structure and Dynamics of Duplex Gna. Authors: Johnson, A.T. / Schlegel, M.K. / Meggers, E. / Essen, L.O. / Wiest, O. #1: ![]() Title: Duplex Structure of a Minimal Nucleic Acid. Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E. #2: ![]() Title: Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna. Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 14.1 KB | Display | ![]() |
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PDB format | ![]() | 9.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.7 KB | Display | ![]() |
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Full document | ![]() | 383.9 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 2155.194 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SYNTHETIC GLYCOL NUCLEIC ACID 3'-((ZCY)P(ZTH)P(ZCY)P(ZBU)P(ZAD)P(ZGU)P(ZAD)P(ZGU))-2' | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | URACIL U4 IS BROMINATED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 10 % MPD, 40 MM SODIUM CACODYLATE, PH 5.5, 20 MM COBALT HEXAMINE, 40 MM LICL, 20 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 24, 2007 / Details: MIRRORS |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91985 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→15.88 Å / Num. obs: 2242 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 17.4 % / Biso Wilson estimate: 34.172 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.83→1.93 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 8.9 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.83→8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.649 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY-EQUIVALENT MOLECULE, 3'TERMINAL CYTOSINE NUCLEOTIDE AND 5-BROMO ATOM AT U4 ONLY PARTIAL OCCUPANCY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.623 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→8 Å
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Refine LS restraints |
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