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Basic information

Entry
Database: PDB / ID: 7jrr
TitleCrystal structures of artificially designed homomeric RNA nanoarchitectures
ComponentsRNA (50-MER)
KeywordsRNA / nano structure / dimeric parallelogram
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0739
Polymers16,6951
Non-polymers3788
Water82946
1
A: RNA (50-MER)
hetero molecules

A: RNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,14618
Polymers33,3902
Non-polymers75616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5270 Å2
ΔGint-100 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.219, 40.219, 202.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-238-

HOH

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Components

#1: RNA chain RNA (50-MER)


Mass: 16694.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES pH 7.0, 20 of mM KCl, 5 mM of MnCl2, 35 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.0879→40.22 Å / Num. obs: 10347 / % possible obs: 96.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 47.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.3
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 614 / CC1/2: 0.3 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000718data reduction
HKL-2000718data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2NOK

2nok


Resolution: 2.16→28.163 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 932 10 %
Rwork0.2261 8388 -
obs0.2295 9320 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.31 Å2 / Biso mean: 57.7634 Å2 / Biso min: 27.63 Å2
Refinement stepCycle: final / Resolution: 2.16→28.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1107 40 46 1193
Biso mean--67.51 51.14 -
Num. residues----50
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051238
X-RAY DIFFRACTIONf_angle_d1.2371929
X-RAY DIFFRACTIONf_chiral_restr0.048254
X-RAY DIFFRACTIONf_plane_restr0.00751
X-RAY DIFFRACTIONf_dihedral_angle_d14.628611
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.16-2.27390.35751080.3585100382
2.2739-2.41630.34021290.3095114696
2.4163-2.60270.34681340.3045119398
2.6027-2.86440.34071370.311122399
2.8644-3.27840.29261370.23951231100
3.2784-4.12830.21721400.19421267100
4.1283-28.1630.22891470.1919132596

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