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- PDB-1rxa: CRYSTAL STRUCTURE OF R(CCCCGGGG) IN TWO DISTINCT LATTICES -

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Basic information

Entry
Database: PDB / ID: 1rxa
TitleCRYSTAL STRUCTURE OF R(CCCCGGGG) IN TWO DISTINCT LATTICES
ComponentsRNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsPortmann, S. / Usman, N. / Egli, M.
CitationJournal: Biochemistry / Year: 1995
Title: The crystal structure of r(CCCCGGGG) in two distinct lattices.
Authors: Portmann, S. / Usman, N. / Egli, M.
History
DepositionMay 5, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,5571
Polymers2,5571
Non-polymers00
Water00
1
A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')

A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,1132
Polymers5,1132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)39.734, 39.734, 58.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain RNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')


Mass: 2556.593 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growMethod: vapor diffusion / pH: 4.5 / Details: pH 4.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4CACL211
5WATER12
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMRNA1drop
250 mMsodium cacodylate1drop
37.8 mMcalcium chloride1drop
415 %MPD1drop
530 %MPD1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.9→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.25 -
obs0.25 710
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 169 0 0 169
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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