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- PDB-9ol1: 16mer self-complementary duplex RNA with dI:s(2)C pair sequence 2 -

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Basic information

Entry
Database: PDB / ID: 9ol1
Title16mer self-complementary duplex RNA with dI:s(2)C pair sequence 2
ComponentsDNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*I)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
KeywordsRNA / Deoxyribo-purine / 2-thiocytidine / deoxyinosine / RNA duplex / Origin of Life
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.243 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2104708 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Biorxiv / Year: 2025
Title: Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension.
Authors: Fang, Z. / Acikgoz, O. / Jia, X. / Essex, J. / Wen, R. / Szostak, J.W.
History
DepositionMay 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*I)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1082
Polymers5,0681
Non-polymers401
Water1,44180
1
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*I)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules

A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*I)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2164
Polymers10,1362
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area1550 Å2
ΔGint-17 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.898, 40.898, 124.979
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21A-249-

HOH

31A-253-

HOH

41A-255-

HOH

51A-269-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*I)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')


Mass: 5068.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.243→34.077 Å / Num. obs: 11727 / % possible obs: 100 % / Redundancy: 17.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.044 / Rrim(I) all: 0.135 / Net I/σ(I): 12.5
Reflection shellResolution: 1.243→1.265 Å / Redundancy: 14.7 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 2 / Num. unique obs: 572 / CC1/2: 0.439 / Rpim(I) all: 0.754 / Rrim(I) all: 2.14 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.243→34.077 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.949 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.229 1173 10.005 %
Rwork0.1864 10551 -
all0.191 --
obs-11724 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å20 Å2
2--0.002 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.243→34.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 1 80 415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011373
X-RAY DIFFRACTIONr_bond_other_d0.0020.019155
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.968578
X-RAY DIFFRACTIONr_angle_other_deg0.7681.82380
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0559
X-RAY DIFFRACTIONr_chiral_restr0.0760.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0258
X-RAY DIFFRACTIONr_nbd_refined0.0860.231
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.2155
X-RAY DIFFRACTIONr_nbtor_refined0.2390.2142
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.275
X-RAY DIFFRACTIONr_metal_ion_refined0.1990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0970.211
X-RAY DIFFRACTIONr_nbd_other0.1470.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.239
X-RAY DIFFRACTIONr_scbond_it1.2561.468373
X-RAY DIFFRACTIONr_scbond_other1.2541.467374
X-RAY DIFFRACTIONr_scangle_it1.8022.684578
X-RAY DIFFRACTIONr_scangle_other1.8012.683579
X-RAY DIFFRACTIONr_lrange_it4.61722.046550
X-RAY DIFFRACTIONr_lrange_other4.03520.561502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.243-1.2750.292850.3137630.318480.9370.9311000.293
1.275-1.310.371820.2987370.3058190.8920.9351000.276
1.31-1.3480.31790.2847170.2877970.9320.94199.87450.258
1.348-1.390.27800.2637220.2638020.9450.951000.234
1.39-1.4350.228760.2346800.2347560.960.961000.204
1.435-1.4850.294730.2166580.2247310.9370.9661000.19
1.485-1.5410.201720.1916480.1927200.9720.9731000.163
1.541-1.6040.225690.1716230.1766920.9670.9811000.153
1.604-1.6750.216660.1685870.1736540.9690.98199.84710.147
1.675-1.7570.198630.1615720.1656350.9760.9841000.154
1.757-1.8520.22620.1765520.186140.970.9811000.168
1.852-1.9640.226560.1945110.1985670.9690.9751000.185
1.964-2.0990.219550.184880.1845430.9730.9781000.179
2.099-2.2660.232510.1824580.1875090.9750.9781000.19
2.266-2.4810.254460.1934180.1994640.9590.9781000.208
2.481-2.7720.266430.1893860.1964290.960.9791000.217
2.772-3.1980.221390.1753470.1793870.9670.98499.74160.219
3.198-3.9080.17320.1442930.1463250.9870.9891000.194
3.908-5.4910.212270.1372410.1432680.9820.991000.191
5.491-34.0770.212170.2151490.2141670.9690.96899.40120.321

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