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- PDB-3p4d: Alternatingly modified 2'Fluoro RNA octamer f/rC4G4 -

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Basic information

Entry
Database: PDB / ID: 3p4d
TitleAlternatingly modified 2'Fluoro RNA octamer f/rC4G4
Components5'-R(*(CFZ)P*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3'
KeywordsRNA / 2'-FLUORO-RNA / O2'-MODIFICATION / OCTAMER / 2'-fluoro 2'-deoxycytidine / 2'-fluoro 2'-deoxyguanosine / siRNA
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.
Authors: Pallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*(CFZ)P*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3'
B: 5'-R(*(CFZ)P*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,1292
Polymers5,1292
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.630, 41.630, 126.489
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
11A-15-

HOH

21B-13-

HOH

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Components

#1: RNA chain 5'-R(*(CFZ)P*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3'


Mass: 2564.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA octamer
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, ...Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, 35%), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 3843 / Num. obs: 3824 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 28.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.9 / Num. unique all: 370 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXB

1rxb


Resolution: 1.85→21.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.824 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27115 280 7.3 %RANDOM
Rwork0.2096 ---
obs0.21426 3544 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.878 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0.58 Å20 Å2
2---1.15 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→21.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 338 0 28 366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021376
X-RAY DIFFRACTIONr_angle_refined_deg2.1243584
X-RAY DIFFRACTIONr_chiral_restr0.1030.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02168
X-RAY DIFFRACTIONr_scbond_it2.1753376
X-RAY DIFFRACTIONr_scangle_it2.7654.5584
LS refinement shellResolution: 1.85→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 23 -
Rwork0.243 243 -
obs-243 100 %
Refinement TLS params.Method: refined / Origin x: 10.6376 Å / Origin y: 9.3828 Å / Origin z: 9.8008 Å
111213212223313233
T0.0474 Å20.0038 Å20.0304 Å2-0.0712 Å20.0313 Å2--0.0929 Å2
L2.8079 °20.5057 °2-0.4315 °2-2.8223 °20.7585 °2--1.0145 °2
S0.1501 Å °-0.2224 Å °-0.1464 Å °0.1378 Å °-0.0481 Å °0.236 Å °-0.0893 Å °-0.0368 Å °-0.102 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 28
2X-RAY DIFFRACTION1A7 - 27
3X-RAY DIFFRACTION1B201 - 208
4X-RAY DIFFRACTION1A101 - 108

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