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- PDB-1i0g: 1.45 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-F... -

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Basic information

Entry
Database: PDB / ID: 1i0g
Title1.45 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-FLUOROETHYL THYMINE IN PLACE OF T6, MEDIUM NA-SALT
Components5'-D(*GP*CP*GP*TP*AP*(125)P*AP*CP*GP*C)-3'
KeywordsDNA / A-form double helix / modified sugar
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTereshko, V. / Wilds, C.J. / Minasov, G. / Prakash, T.P. / Maier, M.A. / Howard, A. / Wawrzak, Z. / Manoharan, M. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
Authors: Tereshko, V. / Wilds, C.J. / Minasov, G. / Prakash, T.P. / Maier, M.A. / Howard, A. / Wawrzak, Z. / Manoharan, M. / Egli, M.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(125)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(125)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2373
Polymers6,2142
Non-polymers231
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.96, 43.57, 45.40
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*AP*(125)P*AP*CP*GP*C)-3'


Mass: 3107.048 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Na, Mg salts, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298 K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMDNA1drop
240 mMalkali metal ions(chloride salt)1drop
320 mMalkaline cacodylate1drop
46 mMspermine1drop
510 mM1dropMgCl2
635 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.8151 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8151 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 8695 / Num. obs: 8695 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.19 -random
Rwork0.159 --
obs0.159 8695 -
all-8695 -
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 1 92 505
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it

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