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- PDB-8ynp: RNA duplex containing Methylformamide -

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Basic information

Entry
Database: PDB / ID: 8ynp
TitleRNA duplex containing Methylformamide
ComponentsRNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3')
KeywordsRNA / Methylformamide
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKondo, J. / Abe, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR18S1 Japan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs.
Authors: Nomura, K. / An, S. / Kobayashi, Y. / Kondo, J. / Shi, T. / Murase, H. / Nakamoto, K. / Kimura, Y. / Abe, N. / Ui-Tei, K. / Abe, H.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 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: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,8952
Polymers7,8952
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint4 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.604, 27.932, 28.668
Angle α, β, γ (deg.)110.030, 114.810, 95.760
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3')


Mass: 3947.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, sodium cacodylate, spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.91962 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91962 Å / Relative weight: 1
ReflectionResolution: 1.4→25.15 Å / Num. obs: 12164 / % possible obs: 93.9 % / Redundancy: 3.576 % / Biso Wilson estimate: 18.341 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.084 / Χ2: 0.963 / Net I/σ(I): 12.58 / Num. measured all: 43501
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.433.7110.2317.0731219428410.950.2789.3
1.43-1.473.6980.2117.6232699488840.9650.24793.2
1.47-1.523.6560.1878.2130388978310.9590.21992.6
1.52-1.563.6040.1668.7629668718230.9650.19694.5
1.56-1.613.4680.1319.927928638050.9840.15593.3
1.61-1.673.2870.10410.4824628097490.9860.12692.6
1.67-1.733.6660.09512.1927908157610.990.11293.4
1.73-1.83.7340.08913.4127527807370.9870.10494.5
1.8-1.883.7160.08613.825127136760.9880.194.8
1.88-1.983.6580.07914.4424957166820.9890.09295.3
1.98-2.083.5890.07114.9322546666280.9920.08494.3
2.08-2.213.5030.06915.3321306366080.9920.08295.6
2.21-2.363.1940.06515.0818146085680.9880.07993.4
2.36-2.553.6530.06316.9419475545330.9930.07496.2
2.55-2.793.7230.06517.3718135124870.990.07695.1
2.79-3.123.5920.07117.4815844594410.9910.08496.1
3.12-3.613.5160.07217.9913894143950.9890.08595.4
3.61-4.423.1630.05517.19873313120.9930.06794.3
4.42-6.253.4940.04918.028912662550.9970.05895.9
6.25-25.153.3450.05317.534951531480.9940.06396.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→25.15 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 1216 10.01 %
Rwork0.1515 10933 -
obs0.1537 12149 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 38.83 Å2 / Biso mean: 13.846 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: final / Resolution: 1.4→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 514 0 170 684
Biso mean---23.29 -
Num. residues----24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.450.21061260.17571135126190
1.45-1.520.19741370.16671233137094
1.52-1.60.20811340.15691207134194
1.6-1.70.18051320.14271194132693
1.7-1.830.15331360.14531222135895
1.83-2.010.16981370.15081230136796
2.01-2.310.18891370.161227136495
2.31-2.90.20171380.17691244138297
2.91-25.150.14041390.13251241138096

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