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- PDB-406d: 5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(BRO) UP*CP*GP*GP*UP*G)-3' -

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Basic information

Entry
Database: PDB / ID: 406d
Title5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(BRO) UP*CP*GP*GP*UP*G)-3'
ComponentsRNA (5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(5BU)P*CP*GP*GP*UP*G)-3')
KeywordsRNA / DISORDERED / DOUBLE HELIX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsShah, S.A. / Brunger, A.T.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure.
Authors: Shah, S.A. / Brunger, A.T.
History
DepositionJun 22, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 5, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Feb 28, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(5BU)P*CP*GP*GP*UP*G)-3')
E: RNA (5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(5BU)P*CP*GP*GP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)11,1082
Polymers11,1082
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.627, 39.627, 91.018
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Number of models2
Components on special symmetry positions
IDModelComponents
11A-18-

HOH

21A-19-

HOH

31A-30-

HOH

41E-35-

HOH

51E-36-

HOH

61E-37-

HOH

71E-38-

HOH

81E-39-

HOH

91E-41-

HOH

101E-42-

HOH

113A-22-

HOH

123A-24-

HOH

133A-35-

HOH

143A-37-

HOH

153A-54-

HOH

163A-103-

HOH

173E-36-

HOH

183E-37-

HOH

193E-38-

HOH

203E-39-

HOH

213E-46-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(1), (-1), (-1)68.64, 182.036

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Components

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


Mass: 5554.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CRYSTAL IS MADE OF STATICALLY DISORDERED 17-BP RNA DUPLEX. ALL CONFIRMATIONS ARE REPRESENTED BY ...THE CRYSTAL IS MADE OF STATICALLY DISORDERED 17-BP RNA DUPLEX. ALL CONFIRMATIONS ARE REPRESENTED BY FOUR MODELS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 38 %
Description: The crystal packing of 17-bp RNA duplex is statically disordered. As a result, the asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of ...Description: The crystal packing of 17-bp RNA duplex is statically disordered. As a result, the asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register, such that backbones superimpose, but base identity differs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 30011
2NACL11
3SODIUM ACETATE11
4PEG 30012
5NACL12
6SODIUM ACETATE12
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 28 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 %(v/v)PEG3001reservoir
2150 mM1reservoirNaCl
3100 mMsodium acetate1reservoir
41
51
61

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
41
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSLS X12B1
2
3
4
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 10, 1995
2
3
4
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDRelative weight
11
21
31
41
ReflectionResolution: 1.8→50 Å / Num. all: 8052 / Num. obs: 8052 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % possible obs: 98.3 %
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.73

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementResolution: 1.8→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 382611.75 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. The structure of statically disordered 17-bp RNA duplex is represented by four models in the asymmetric unit, each model for a distinct conformation of the duplex. ...Details: BULK SOLVENT MODEL USED. The structure of statically disordered 17-bp RNA duplex is represented by four models in the asymmetric unit, each model for a distinct conformation of the duplex. The sum of all models contribute to the observed diffraction data. To generate the contents of the entire asymmetric unit from the four disordered duplexes, a strict non-crystallographic hypersymmetry was applied.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1524 10.5 %RANDOM
Rwork0.262 ---
obs0.262 14484 97.7 %-
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.53 Å20 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 726 0 34 760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d10.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 227 9.8 %
Rwork0.264 2079 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP.PADNA-RNA_REP.PARAM
X-RAY DIFFRACTION2BR.PAR
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor obs: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.03
LS refinement shell
*PLUS
Rfactor obs: 0.264

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