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- PDB-6ual: A Self-Assembling DNA Crystal Scaffold with Cavities Containing 3... -

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Basic information

Entry
Database: PDB / ID: 6ual
TitleA Self-Assembling DNA Crystal Scaffold with Cavities Containing 3 Helical Turns per Edge
Components
  • DNA (32-MER)
  • DNA (5'-D(*TP*GP*GP*AP*AP*AP*CP*AP*GP*AP*CP*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*G)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.514 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
CitationJournal: To Be Published
Title: Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry
Authors: Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
History
DepositionSep 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (32-MER)
C: DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*G)-3')
A: DNA (5'-D(*TP*GP*GP*AP*AP*AP*CP*AP*GP*AP*CP*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)19,5924
Polymers19,5924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.251, 179.251, 48.138
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: DNA chain DNA (32-MER)


Mass: 9718.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')


Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*AP*G)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*GP*GP*AP*AP*AP*CP*AP*GP*AP*CP*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')


Mass: 6207.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 7.6 Å3/Da / Density % sol: 83.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M cacodylate pH 7.0, 20 mM MgCl2, 1mM spermine, 1.0 mM cobalt hexamine, 15% ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2018
RadiationMonochromator: double crystal si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.514→50 Å / Num. obs: 3195 / % possible obs: 95.1 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.034 / Rrim(I) all: 0.104 / Χ2: 4.623 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.514-4.587.10.7771110.8670.2940.8330.55573
4.58-4.667.10.8351380.8190.3260.8990.50580.7
4.66-4.757.70.7971480.8380.290.850.5682.2
4.75-4.857.50.6391450.8820.2350.6830.53990.6
4.85-4.9580.5531550.930.1970.5890.59393.9
4.95-5.077.90.4621540.9620.1670.4920.67993.3
5.07-5.1980.4011700.9530.1460.4270.83795
5.19-5.338.30.3371580.970.1210.3581.21995.8
5.33-5.498.80.3211730.9770.1130.3411.029100
5.49-5.678.50.2921530.9720.1040.311.329100
5.67-5.878.40.2561790.9850.0930.2732.191100
5.87-6.117.80.2371720.9760.090.2532.09999.4
6.11-6.388.30.2141620.9770.0780.2282.349100
6.38-6.729.60.1851760.9940.0630.1962.386100
6.72-7.148.80.1511610.9950.0530.163.638100
7.14-7.699.30.141680.9910.0480.1486.026100
7.69-8.4610.80.1211680.9950.0390.1288.793100
8.46-9.6710.80.1141740.9960.0370.1212.733100
9.67-12.1610.50.11660.9980.0330.10512.843100
12.16-509.80.0771640.9980.0270.08216.81897

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.514→45.978 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 35.03
RfactorNum. reflection% reflection
Rfree0.2427 158 4.96 %
Rwork0.1974 --
obs0.1993 3183 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 589.29 Å2 / Biso min: 112.72 Å2
Refinement stepCycle: final / Resolution: 4.514→45.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1306 0 0 1306
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051462
X-RAY DIFFRACTIONf_angle_d0.6792248
X-RAY DIFFRACTIONf_chiral_restr0.043254
X-RAY DIFFRACTIONf_plane_restr0.00364
X-RAY DIFFRACTIONf_dihedral_angle_d31.541626
LS refinement shellResolution: 4.5141→45.9805 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2427 158 -
Rwork0.1974 3025 -
obs--94 %

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