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- PDB-259d: RNA HYDRATION: A DETAILED LOOK -

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Basic information

Entry
Database: PDB / ID: 259d
TitleRNA HYDRATION: A DETAILED LOOK
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 / SYNCHROTRON / Resolution: 1.46 Å
AuthorsEgli, M. / Portmann, S. / Usman, N.
Citation
Journal: Biochemistry / Year: 1996
Title: RNA hydration: a detailed look.
Authors: Egli, M. / Portmann, S. / Usman, N.
#1: Journal: Biochemistry / Year: 1995
Title: Crystal Structure of r(CCCCGGGG) in Two Distinct Lattices
Authors: Portmann, S. / Usman, N. / Egli, M.
History
DepositionMay 3, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 26, 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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*GP*G)-3')
B: 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
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.260, 42.260, 130.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-35-

HOH

21A-57-

HOH

31A-59-

HOH

41A-61-

HOH

51A-69-

HOH

61A-75-

HOH

71A-94-

HOH

81A-96-

HOH

91B-21-

HOH

101B-23-

HOH

111B-26-

HOH

121B-40-

HOH

131B-84-

HOH

141B-89-

HOH

151B-125-

HOH

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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.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6 / Details: pH 4.60, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA ACETATE11
3NH4 SULFATE11
4WATER12
5NA ACETATE12
6NH4 SULFATE12
Crystal grow
*PLUS
pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMRNA oligonucleotide1drop
250 mMsodium acetate1drop
31 Mammonium sulfate1drop
4100 mMsodium acetate1reservoir
52 Mammonium sulfate1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 23, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.46 Å / Num. obs: 8040 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.051
Reflection
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 10 Å / % possible obs: 99.6 %
Reflection shell
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 1.49 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 25.7

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.46→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.263 --
Rwork0.201 --
obs0.201 7858 99.6 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.46→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 338 0 113 451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.46→1.49 Å /
Rfactor% reflection
Rwork0.369 -
obs-97.1 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.369

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