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- PDB-6cxz: RNA octamer containing 2'-F, 4'-Calpha-Me U. -

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Basic information

Entry
Database: PDB / ID: 6cxz
TitleRNA octamer containing 2'-F, 4'-Calpha-Me U.
ComponentsRNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3')
KeywordsRNA / oligonucleotide / modified base
Function / homologyCACODYLATE ION / COBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity.
Authors: Harp, J.M. / Guenther, D.C. / Bisbe, A. / Perkins, L. / Matsuda, S. / Bommineni, G.R. / Zlatev, I. / Foster, D.J. / Taneja, N. / Charisse, K. / Maier, M.A. / Rajeev, K.G. / Manoharan, M. / Egli, M.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3')
B: RNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3834
Polymers5,0852
Non-polymers2982
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-3 kcal/mol
Surface area3370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.460, 30.460, 81.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

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Components

#1: RNA chain RNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3')


Mass: 2542.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0 mM RNA, 40 mM Na cacodylate, 20 mM magnesium chloride, 20 mM cobalt(3+) hexamine chloride, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 6684 / % possible obs: 99.8 % / Redundancy: 21.6 % / Biso Wilson estimate: 14.34 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.022 / Rrim(I) all: 0.104 / Χ2: 1.048 / Net I/σ(I): 8.7 / Num. measured all: 145275
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.539.50.9883280.8080.3131.041.05799.7
1.53-1.5512.70.873190.8610.2410.9051.08599.7
1.55-1.58160.7343180.9550.1830.7571.08899.7
1.58-1.6219.20.6783330.9690.1560.6961.09499.7
1.62-1.6522.30.6033220.9790.130.6171.08799.7
1.65-1.6923.70.4593310.990.0950.4691.09100
1.69-1.7324.10.3613130.9950.0740.3691.095100
1.73-1.7823.70.3213400.9930.0660.3281.072100
1.78-1.8321.20.2963220.990.0650.3041.095100
1.83-1.89210.2563400.9920.0570.2631.064100
1.89-1.9625.50.223170.9940.0440.2251.046100
1.96-2.0426.10.1783440.9960.0350.1821.076100
2.04-2.1325.60.1463280.9970.0290.1491.058100
2.13-2.2425.50.1323330.9980.0260.1341.021100
2.24-2.38250.1163450.9980.0230.1180.998100
2.38-2.5624.70.0963360.9980.020.0981.04399.4
2.56-2.8223.80.0813470.9990.0170.0831.016100
2.82-3.2321.40.0683390.9980.0150.071.01298
3.23-4.0719.20.0543590.9990.0130.0561.00399.4
4.07-2521.10.0524170.9990.0120.0530.922100

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.13_2992refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VR4

5vr4


Resolution: 1.5→24.439 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.27 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2154 519 4.42 %
Rwork0.1864 --
obs0.1877 6672 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.05 Å2 / Biso mean: 21.2079 Å2 / Biso min: 12.67 Å2
Refinement stepCycle: final / Resolution: 1.5→24.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 336 12 51 399
Biso mean--28.69 33.27 -
Num. residues----16
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4996-1.65050.30341230.24262801292499
1.6505-1.88920.19251250.185228462971100
1.8892-2.37990.21811300.196628032933100
2.3799-24.44220.2071410.17222780292199

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