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Basic information

Entry
Database: PDB / ID: 7jrt
TitleCrystal structures of artificially designed homomeric RNA nanoarchitectures
ComponentsRNA nano bracelet
KeywordsRNA / nano structure / dimeric parallelogram
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsLiu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1555361 United States
CitationJournal: Sci Adv / Year: 2021
Title: Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.
Authors: Liu, D. / Shao, Y. / Piccirilli, J.A. / Weizmann, Y.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: 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 / _citation_author.identifier_ORCID
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: RNA nano bracelet
B: RNA nano bracelet


Theoretical massNumber of molelcules
Total (without water)86,5162
Polymers86,5162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-4 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.436, 71.990, 89.439
Angle α, β, γ (deg.)90.000, 117.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA nano bracelet


Mass: 43257.762 Da / Num. of mol.: 2 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80 mM NaCl, 12 mM KCl, 20 mM MgCl2, 40 mM sodium cacodylate pH 6.0, 30 % (v/v) MPD, 12 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.1048 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1048 Å / Relative weight: 1
ReflectionResolution: 3.07→45.53 Å / Num. obs: 18129 / % possible obs: 99.3 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 39.2
Reflection shellResolution: 3.07→3.18 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 1817

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000718data reduction
HKL-2000718data scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2NOK

2nok


Resolution: 3.07→45.53 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1758 9.7 %
Rwork0.1886 16371 -
obs0.1924 18129 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.15 Å2 / Biso mean: 86.65 Å2 / Biso min: 26.04 Å2
Refinement stepCycle: final / Resolution: 3.07→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5730 0 0 5730
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066408
X-RAY DIFFRACTIONf_angle_d1.229988
X-RAY DIFFRACTIONf_chiral_restr0.0731340
X-RAY DIFFRACTIONf_plane_restr0.006268
X-RAY DIFFRACTIONf_dihedral_angle_d15.0293210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.07-3.1530.28781260.2409123396
3.153-3.24570.27541230.2158123798
3.2457-3.35050.24671350.2101123798
3.3505-3.47020.28781460.2194123898
3.4702-3.60910.27551290.2055125097
3.6091-3.77330.26251450.1967124899
3.7733-3.97210.20641380.1795126399
3.9721-4.22080.2271370.1836125199
4.2208-4.54640.21831290.1958128299
4.5464-5.00340.26381340.2013125999
5.0034-5.72620.23071490.17861268100
5.7262-7.20980.21511350.1936128799
7.2098-45.530.1811320.1636131899

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