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- PDB-4jrd: Crystal structure of the parallel double-stranded helix of poly(A) RNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jrd | ||||||||||||||||||
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Title | Crystal structure of the parallel double-stranded helix of poly(A) RNA | ||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / PARALLEL DOUBLE HELIX / POLY(A) / MRNA / PABP / Poly(A) motif | Function / homology | AMMONIUM ION / RNA / RNA (> 10) | ![]() Method | ![]() ![]() ![]() Safaee, N. / Noronha, A.M. / Kozlov, G. / Rodionov, D. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K. | ![]() ![]() Title: Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction. Authors: Safaee, N. / Noronha, A.M. / Rodionov, D. / Kozlov, G. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.8 KB | Display | ![]() |
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PDB format | ![]() | 27.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
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Full document | ![]() | 419.5 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.6 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 3576.306 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NH4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.49 Å3/Da / Density % sol: 17.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR ...Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1→41 Å / Num. all: 23042 / Num. obs: 22972 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): -3 / Redundancy: 2.73 % / Rmerge(I) obs: 0.0944 / Net I/σ(I): 34.35 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1→1.1 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.1419 / Mean I/σ(I) obs: 4.72 / % possible all: 73.1 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→41 Å / Num. parameters: 5165 / Num. restraintsaints: 6773 / Cross valid method: FREE R / σ(F): 1
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 242 / Occupancy sum non hydrogen: 571 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→41 Å
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Refine LS restraints |
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