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- PDB-8f24: Mirror-image RNA octamer containing 2'-OMe-L-uridine -

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Basic information

Entry
Database: PDB / ID: 8f24
TitleMirror-image RNA octamer containing 2'-OMe-L-uridine
ComponentsMirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
KeywordsRNA / Mirror-image RNA
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDantsu, Y. / Zhang, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: Derivatization of Mirror-Image l-Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization.
Authors: Dantsu, Y. / Zhang, W.
History
DepositionNov 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Polymer sequence / Structure summary
Category: entity / entity_poly ...entity / entity_poly / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle
Item: _entity.formula_weight / _entity_poly.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
A: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
E: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
D: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
B: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
F: Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,72411
Polymers15,2446
Non-polymers4805
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.070, 47.070, 365.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21B-101-

SO4

31C-103-

HOH

41A-204-

HOH

51A-205-

HOH

61A-206-

HOH

71D-101-

HOH

81F-202-

HOH

91F-206-

HOH

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Components

#1: RNA chain
Mirror-image RNA 0G-XEC-0G-0U-0A-0C-0A-0C


Mass: 2540.588 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.73 % / Description: diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 2795 / % possible obs: 98.5 % / Redundancy: 8.2 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Rsym value: 0.068 / Χ2: 1.185 / Net I/σ(I): 30.1
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 709 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.224 / Rrim(I) all: 0.903 / Rsym value: 0.675 / Χ2: 1.088 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KW4

7kw4


Resolution: 3.2→19.94 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.835 / SU B: 20.47 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29824 277 9.9 %RANDOM
Rwork0.21338 ---
obs0.2215 2534 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 3.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms672 0 217 19 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026979
X-RAY DIFFRACTIONr_bond_other_d0.0440.03488
X-RAY DIFFRACTIONr_angle_refined_deg2.5012.8741510
X-RAY DIFFRACTIONr_angle_other_deg3.2663.561135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021459
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023143
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.592.033977
X-RAY DIFFRACTIONr_scbond_other0.5872.014958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.973.021480
X-RAY DIFFRACTIONr_long_range_B_refined2.71120.2531294
X-RAY DIFFRACTIONr_long_range_B_other2.66220.2431294
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 18 -
Rwork0.259 158 -
obs--94.62 %

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