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- PDB-36ll: 16mer self-complementary RNA duplex with L-U -

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Basic information

Entry
Database: PDB / ID: 36ll
Title16mer self-complementary RNA duplex with L-U
ComponentsRNA (16-mer)
KeywordsRNA / Nonenzymatic RNA replication / Chirality
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsEssex, J. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)2325198 United States
CitationJournal: To Be Published
Title: Effects of Chemically Activated L-Nucleotides on Nonenzymatic RNA Copying
Authors: Essex, J. / Jia, X. / Zhang, J. / Szostak, J.W.
History
DepositionJun 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (16-mer)


Theoretical massNumber of molelcules
Total (without water)5,0951
Polymers5,0951
Non-polymers00
Water82946
1
A: RNA (16-mer)

A: RNA (16-mer)


Theoretical massNumber of molelcules
Total (without water)10,1902
Polymers10,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.091, 42.091, 130.113
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-121-

HOH

21A-125-

HOH

31A-131-

HOH

41A-138-

HOH

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Components

#1: RNA chain RNA (16-mer)


Mass: 5095.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30%v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2025
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→24.27 Å / Num. obs: 8765 / % possible obs: 89.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.67 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.3
Reflection shellResolution: 1.35→1.44 Å / Num. unique obs: 438 / CC1/2: 0.552

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→24.27 Å / SU ML: 0.1868 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.4503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 877 10.01 %
Rwork0.2395 7882 -
obs0.2409 8759 86.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.93 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 217 120 46 383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054377
X-RAY DIFFRACTIONf_angle_d1.0739587
X-RAY DIFFRACTIONf_chiral_restr0.054377
X-RAY DIFFRACTIONf_plane_restr0.009621
X-RAY DIFFRACTIONf_dihedral_angle_d22.6225229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.440.4003410.2927371X-RAY DIFFRACTION24.95
1.44-1.550.31881590.30981431X-RAY DIFFRACTION96.36
1.55-1.70.33711640.30061482X-RAY DIFFRACTION99.94
1.7-1.950.27361680.27861504X-RAY DIFFRACTION99.94
1.95-2.450.31911700.29511521X-RAY DIFFRACTION100
2.46-24.270.20611750.19561573X-RAY DIFFRACTION97.98

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