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Open data
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Basic information
Entry | Database: PDB / ID: 430d | ||||||
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Title | STRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RRNA | ||||||
![]() | SARCIN/RICIN LOOP FROM RAT 28S R-RNA | ||||||
![]() | RNA / U-RNA / DOUBLE HELIX / HAIRPIN / BLUNT STEM / TETRALOOP MISMATCHED / BASE TRIPLE / RIBONUCLEIC ACID | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Correll, C.C. / Munishkin, A. / Chan, Y.L. / Ren, Z. / Wool, I.G. / Steitz, T.A. | ||||||
![]() | ![]() Title: Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Authors: Correll, C.C. / Munishkin, A. / Chan, Y.L. / Ren, Z. / Wool, I.G. / Steitz, T.A. #1: ![]() Title: The Conformation of the Sarcin/Ricin Loop from 28S Ribosomal RNA Authors: Szewczak, A.A. / Moore, P.B. / Chan, Y.L. / Wool, I.G. #2: ![]() Title: The Sarcin/Ricin Loop, a Modular RNA Authors: Szewczak, A.A. / Moore, P.B. #3: ![]() Title: Comparison of the Crystal and Solution Structure of Two RNA Oligonucleotides Authors: Rife, J.P. / Stallings, S.C. / Correll, C.C. / Dallas, A. / Steitz, T.A. / Moore, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.6 KB | Display | ![]() |
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PDB format | ![]() | 18 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 342.4 KB | Display | ![]() |
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Full document | ![]() | 344.4 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 3.2 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: 9455.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Nov 15, 1997 / Details: SILICON 111 BENDING MIRRO |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 5854 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.217 / % possible all: 88.8 |
Reflection | *PLUS Num. obs: 6036 / % possible obs: 92.7 % / Num. measured all: 22518 |
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Processing
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Refinement | Method to determine structure: MAD PHASING METHOD / Resolution: 2.1→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 30991867.71 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 60.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Rfactor Rfree error: 0.092 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Rfactor obs: 0.28 / Rfactor Rfree: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å |