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- PDB-150d: GUANINE.1,N6-ETHENOADENINE BASE-PAIRS IN THE CRYSTAL STRUCTURE OF... -

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Entry
Database: PDB / ID: 150d
TitleGUANINE.1,N6-ETHENOADENINE BASE-PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(EDA)GCG)
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDA)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
MethodX-RAY DIFFRACTION / 2.25 Å resolution
AuthorsLeonard, G.A. / McAuley-Hecht, K.E. / Gibson, N.J. / Brown, T. / Watson, W.P. / Hunter, W.N.
CitationJournal: Biochemistry / Year: 1994
Title: Guanine-1,N6-ethenoadenine base pairs in the crystal structure of d(CGCGAATT(epsilon dA)GCG).
Authors: Leonard, G.A. / McAuley-Hecht, K.E. / Gibson, N.J. / Brown, T. / Watson, W.P. / Hunter, W.N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 2, 1993 / Release: May 31, 1994
RevisionDateData content typeGroupProviderType
1.0May 31, 1994Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,4473
Polyers7,4232
Non-polymers241
Water2,306128
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)24.311, 39.648, 63.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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


Mass: 3711.438 Da / Num. of mol.: 2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 / Density percent sol: 39.91 %
Crystal growTemp: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
components of the solutions
IDNameCrystal IDSol ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12

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Data collection

DiffractionMean temperature: 297 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionD resolution high: 2.25 Å / Number all: 12357 / Number obs: 9932 / Observed criterion sigma I: 0.5
Reflection
*PLUS
D resolution high: 2.25 Å / Percent possible obs: 94 / Rmerge I obs: 0.032 / Observed criterion sigma I: 0.5

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Processing

Software
NameClassification
X-PLORrefinement
NUCLSQrefinement
RefineSigma F: 2
Least-squares processR factor R work: 0.182 / R factor obs: 0.182 / Highest resolution: 2.25 Å / Lowest resolution: 7 Å / Number reflection obs: 2837
Refine B iso
ClassRefine IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine hist #LASTHighest resolution: 2.25 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 490 / Ligand: 11 / Solvent: 122 / Total: 623
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
R factor R work: 0.182 / R factor obs: 0.182 / Highest resolution: 2.25 Å / Lowest resolution: 7 Å

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