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- PDB-1zff: TTC Duplex B-DNA -

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Basic information

Entry
Database: PDB / ID: 1zff
TitleTTC Duplex B-DNA
Components5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3'
KeywordsDNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsHays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: How sequence defines structure: a crystallographic map of DNA structure and conformation.
Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,0451
Polymers3,0451
Non-polymers00
Water00
1
A: 5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3'

A: 5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)34.292, 20.318, 33.482
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.

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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: 1.78 Å3/Da / Density % sol: 30.74 %
Crystal growTemperature: 298 K / pH: 7
Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2CaCl211
3Spermine11
4MPD11
5H2O11
6Na Cacodylate12
7CaCl212
8MPD12
9H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 0.94→7.9 Å / Num. obs: 11437 / % possible obs: 81.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.2
Reflection shellResolution: 0.94→0.97 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.3 / % possible all: 41.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
REFMAC5.2.0005refinement
EPMRphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY BD0034

Resolution: 0.94→7.72 Å / Cor.coef. Fo:Fc: 0.445 / Cor.coef. Fo:Fc free: 0.43 / Rfactor Rfree error: 0.013 / SU B: 5.5 / SU ML: 0.136 / Data cutoff high absF: 42618.16 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE IS NOT FULLY REFINED TO ITS LOWEST R VALUES! THIS STRUCTURE WILL BE UPDATED AS THE STRUCTURE BECOMES BETTER REFINED. REFER TO MANUSCRIPT CITATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.444 1133 10.3 %RANDOM
Rwork0.428 ---
obs0.428 10948 82.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 0.94→7.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 0 202
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.0040.021
X-RAY DIFFRACTIONc_angle_deg1.283
X-RAY DIFFRACTIONc_scbond_it0.2553
X-RAY DIFFRACTIONc_scangle_it0.4544.5
LS refinement shellResolution: 0.94→1 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 142 10.6 %
Rwork0.456 1202 -
obs--60.8 %

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