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Open data
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Basic information
Entry | Database: PDB / ID: 364d | |||||||||
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Title | 3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA | |||||||||
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![]() | RNA / U-RNA / DOUBLE HELIX / KINKED / INTERNAL LOOP / OVERHANGING BASE / MODIFIED / MISMATCHED | |||||||||
Function / homology | RNA / RNA (> 10)![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Correll, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A. | |||||||||
![]() | ![]() Title: Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Authors: Correll, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A. #1: ![]() Title: Use of Chemically Modified Nucleotides to Determine a 62-Nucleotide RNA Crystal Structure: A Survey of Phosphorothioates, Br, Pt, and Hg Authors: Correll, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A. #2: ![]() Title: The Solution Structure of the Loop E/Loop D Region of E. Coli 5S rRNA Authors: Dallas, 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 | ![]() | 45.7 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 352.7 KB | Display | ![]() |
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Full document | ![]() | 361 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 3530.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: RNA chain | Mass: 6166.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: RNA chain | Mass: 10012.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.4 / Details: pH 6.40, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / 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: PRINCETON 2K / Detector: CCD / Date: Mar 28, 1995 / Details: SILICON 111 BENDING MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.98→20 Å / Num. obs: 4950 / % possible obs: 82.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 47.5 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 82.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: TARGET FOR REFINEMENT WAS MLF: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
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Displacement parameters | Biso mean: 83.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. reflection obs: 4950 / % reflection Rfree: 10.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5.1 % |