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- PDB-3v07: Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid -

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Basic information

Entry
Database: PDB / ID: 3v07
TitleCrystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3')
KeywordsDNA / A-form DNA / 3'-fluoro hexitol nucleic acid / FHNA / R-6'-Me-FHNA / antisense oligonucleotides
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Biochemistry / Year: 2012
Title: Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.
Authors: Pallan, P.S. / Yu, J. / Allerson, C.R. / Swayze, E.E. / Seth, P. / Egli, M.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1822
Polymers6,1822
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-2 kcal/mol
Surface area3770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.302, 43.481, 45.530
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*(F6H)P*AP*CP*GP*C)-3')


Mass: 3091.049 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM sodium cacodylate, 80 mM sodium chloride, 12 mM spermine tetrahydrochloride, 10% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.24→31.45 Å / Num. all: 15944 / Num. obs: 15617 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 47
Reflection shellResolution: 1.24→1.27 Å / % possible all: 88.1

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
CCP4model building
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.24→31.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.361 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.044 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20723 776 5 %RANDOM
Rwork0.15941 ---
obs0.16169 14841 98.17 %-
all-15944 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.337 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---1.03 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.24→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 0 80 490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.021454
X-RAY DIFFRACTIONr_angle_refined_deg2.6083688
X-RAY DIFFRACTIONr_chiral_restr0.4110.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0350.02210
X-RAY DIFFRACTIONr_scbond_it3.113454
X-RAY DIFFRACTIONr_scangle_it3.8964.5688
X-RAY DIFFRACTIONr_rigid_bond_restr2.7783454
LS refinement shellResolution: 1.24→1.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 57 -
Rwork0.205 959 -
obs--88.12 %

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