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- PDB-3q61: 3'-Fluoro Hexitol Nucleic Acid DNA Structure -

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Basic information

Entry
Database: PDB / ID: 3q61
Title3'-Fluoro Hexitol Nucleic Acid DNA Structure
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3')
KeywordsDNA / A-FORM DNA / 3'-Fluoro Hexitol Nucleic Acid / FHNA / Antisense oligonucleotides
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSeth, P.R. / Allerson, C.R. / Prakash, T.P. / Siwkowski, A. / Berdeja, A. / Yu, J. / Pallan, P.S. / Watt, A.T. / Gaus, H. / Bhat, B. ...Seth, P.R. / Allerson, C.R. / Prakash, T.P. / Siwkowski, A. / Berdeja, A. / Yu, J. / Pallan, P.S. / Watt, A.T. / Gaus, H. / Bhat, B. / Egli, M. / Swayze, E.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides.
Authors: Egli, M. / Pallan, P.S. / Allerson, C.R. / Prakash, T.P. / Berdeja, A. / Yu, J. / Lee, S. / Watt, A. / Gaus, H. / Bhat, B. / Swayze, E.E. / Seth, P.P.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1542
Polymers6,1542
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-1 kcal/mol
Surface area3750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.014, 43.134, 45.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3')


Mass: 3077.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized oligonucleotide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM sodium cacodylate, 6 mM sodium chloride, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.56→31.31 Å / Num. all: 7883 / Num. obs: 7849 / % possible obs: 99.56 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.5
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 11.3 / Num. unique all: 791 / % possible all: 100

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Processing

Software
NameVersionClassification
MD2data collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.56→31.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.745 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20887 384 4.7 %RANDOM
Rwork0.16407 ---
obs0.16608 7849 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.373 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.56→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 76 484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021452
X-RAY DIFFRACTIONr_angle_refined_deg2.1173684
X-RAY DIFFRACTIONr_chiral_restr0.1370.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.02210
X-RAY DIFFRACTIONr_scbond_it3.563452
X-RAY DIFFRACTIONr_scangle_it4.2654.5684
X-RAY DIFFRACTIONr_rigid_bond_restr2.9443452
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 34 -
Rwork0.135 545 -
obs--99.48 %

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