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- PDB-3ifi: 2'-SeMe-dG modified octamer DNA -

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Basic information

Entry
Database: PDB / ID: 3ifi
Title2'-SeMe-dG modified octamer DNA
ComponentsDNA (5'-D(*GP*TP*(XUG)P*TP*AP*CP*AP*C)-3')
KeywordsDNA / Selenium / nucleic acid / guanosine
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSheng, J. / Gan, J. / Salon, J. / Huang, Z.
CitationJournal: J.Org.Chem. / Year: 2010
Title: Synthesis and crystal structure of 2'-se-modified guanosine containing DNA.
Authors: Salon, J. / Sheng, J. / Gan, J. / Huang, Z.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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*TP*(XUG)P*TP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,5201
Polymers2,5201
Non-polymers00
Water82946
1
A: DNA (5'-D(*GP*TP*(XUG)P*TP*AP*CP*AP*C)-3')

A: DNA (5'-D(*GP*TP*(XUG)P*TP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0392
Polymers5,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-11
Buried area1990 Å2
ΔGint3 kcal/mol
Surface area2860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.641, 41.641, 24.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe DNA was synthesized by solid phase synthesis and purified by HPLC

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Components

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


Mass: 2519.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by solid phase synthesis
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v / v MPD, 40 mM Na Cacodylate pH 6.0, 12 mM Spermine tetra-HCl, 80 mM Strontium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2009
RadiationMonochromator: Si(lll) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 7069 / Num. obs: 6376 / % possible obs: 90.2 % / Redundancy: 13 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 52.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.16 / Num. unique all: 160 / % possible all: 47.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DNS

1dns


Resolution: 1.2→29.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.333 / SU ML: 0.029 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 295 4.8 %RANDOM
Rwork0.202 ---
all0.203 6693 --
obs0.203 5901 88.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.053 Å0.052 Å
Luzzati sigma a-0.029 Å
Refinement stepCycle: LAST / Resolution: 1.2→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 46 209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.1443279
X-RAY DIFFRACTIONr_chiral_restr0.0580.231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0284
X-RAY DIFFRACTIONr_nbd_refined0.1270.254
X-RAY DIFFRACTIONr_nbtor_refined0.2640.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.224
X-RAY DIFFRACTIONr_scbond_it0.6893264
X-RAY DIFFRACTIONr_scangle_it1.0624.5279
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 7 -
Rwork0.389 205 -
obs--42.15 %
Refinement TLS params.Method: refined / Origin x: -9.6953 Å / Origin y: -50.911 Å / Origin z: -9.7843 Å
111213212223313233
T-0.0079 Å2-0.0044 Å2-0.0103 Å2--0.0162 Å20.0038 Å2---0.0186 Å2
L0.7155 °2-0.804 °20.5378 °2-5.3834 °2-2.4567 °2--2.0558 °2
S-0.0886 Å °-0.0502 Å °-0.0335 Å °0.2587 Å °0.1346 Å °0.0689 Å °-0.1269 Å °0.0141 Å °-0.046 Å °

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