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- PDB-7kw4: L-DNA containing 2'-fluoro modification -

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Basic information

Entry
Database: PDB / ID: 7kw4
TitleL-DNA containing 2'-fluoro modification
ComponentsDNA (5'-D(*(0DG)P*(0FU)P*(0DG)P*(0DT)P*(0DA)P*(0DC)P*(0DA)P*(0DC))-3')
KeywordsDNA / L-DNA / Fluoro modification
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsZhang, W. / Zhang, Y.
CitationJournal: Org.Lett. / Year: 2021
Title: Synthesis and Structural Characterization of 2'-Deoxy-2'-fluoro-l-uridine Nucleic Acids.
Authors: Dantsu, Y. / Zhang, Y. / Zhang, W.
History
DepositionNov 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*(0DG)P*(0FU)P*(0DG)P*(0DT)P*(0DA)P*(0DC)P*(0DA)P*(0DC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4392
Polymers2,4151
Non-polymers241
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.330, 32.330, 75.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

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Components

#1: DNA chain DNA (5'-D(*(0DG)P*(0FU)P*(0DG)P*(0DT)P*(0DA)P*(0DC)P*(0DA)P*(0DC))-3')


Mass: 2414.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 64.74 % / Description: rod-shaped crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.08 M NaCl, 0.02 M MgCl2, 0.04 M Sodium Cacodylate trihydrate pH 5.5, 35% (v/v) MPD, 0.002 M hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.03→28 Å / Num. obs: 12016 / % possible obs: 97.8 % / Redundancy: 29.4 % / Biso Wilson estimate: 9.81 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.025 / Rrim(I) all: 0.143 / Net I/σ(I): 19.9
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 398 / CC1/2: 0.346 / Rpim(I) all: 0.562 / % possible all: 65.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d79

1d79


Resolution: 1.03→22.497 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 546 4.57 %RANDOM
Rwork0.1665 ---
obs0.1668 11951 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.03→22.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 1 54 216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.051180
X-RAY DIFFRACTIONf_angle_d4.65276
X-RAY DIFFRACTIONf_dihedral_angle_d29.94986
X-RAY DIFFRACTIONf_chiral_restr0.43630
X-RAY DIFFRACTIONf_plane_restr0.0548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0301-1.13380.24071290.19912529X-RAY DIFFRACTION90
1.1338-1.29780.14581300.1432879X-RAY DIFFRACTION100
1.2978-1.63510.14891430.16482891X-RAY DIFFRACTION100
1.6351-22.4970.1821440.16813106X-RAY DIFFRACTION100

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