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- PDB-8skw: MicroED structure of d(CGCGCG)2 Z-DNA -

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Basic information

Entry
Database: PDB / ID: 8skw
TitleMicroED structure of d(CGCGCG)2 Z-DNA
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA
Function / homologySPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.1 Å
AuthorsHaymaker, A. / Bardin, A.A. / Martynowycz, M.W. / Nannenga, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136508 United States
CitationJournal: Structure / Year: 2023
Title: Structure determination of a DNA crystal by MicroED.
Authors: Alison Haymaker / Andrey A Bardin / Tamir Gonen / Michael W Martynowycz / Brent L Nannenga /
Abstract: Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In ...Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
History
DepositionApr 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area2570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.280, 32.000, 41.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Z-DNA / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 0.003 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM diffraction shellResolution: 1.1→1.16 Å / Fourier space coverage: 97.9 % / Multiplicity: 9 / Num. of structure factors: 2564 / Phase residual: 24.07 °
EM diffraction statsFourier space coverage: 98.9 % / High resolution: 1.1 Å / Num. of intensities measured: 95258 / Num. of structure factors: 10374 / Phase error rejection criteria: 20 / Rmerge: 25.8
ReflectionBiso Wilson estimate: 9.68 Å2

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Processing

Software
NameVersionClassificationNB
phenix.refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 18.28 Å / B: 32 Å / C: 41.67 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER
RefinementResolution: 1.1→25.38 Å / SU ML: 0.1283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.38
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 968 5.11 %
Rwork0.2098 17976 -
obs0.2105 18944 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.16 Å2
Refinement stepCycle: LAST / Resolution: 1.1→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 33 287
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0198321
ELECTRON CRYSTALLOGRAPHYf_angle_d1.7587486
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.067953
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.017614
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d30.2547145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.160.30031370.27422564ELECTRON CRYSTALLOGRAPHY97.86
1.16-1.230.26681360.24692580ELECTRON CRYSTALLOGRAPHY98.66
1.23-1.330.29321350.24912556ELECTRON CRYSTALLOGRAPHY98.97
1.33-1.460.25241410.24512575ELECTRON CRYSTALLOGRAPHY99.23
1.46-1.670.21631420.21472572ELECTRON CRYSTALLOGRAPHY98.51
1.67-2.10.19721370.18382555ELECTRON CRYSTALLOGRAPHY98.93
2.1-25.380.20621400.19292574ELECTRON CRYSTALLOGRAPHY98.8

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