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- PDB-5do5: Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate -

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Basic information

Entry
Database: PDB / ID: 5do5
TitleCrystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')
KeywordsRNA / 2'-fluoro-RNA / phosphorodithioate RNA / PS2-RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086937 United States
CitationJournal: To Be Published
Title: Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate
Authors: Pallan, P.S. / Egli, M.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Refinement description
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,8871
Polymers3,8871
Non-polymers00
Water1,20767
1
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')

A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,7752
Polymers7,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area4510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.237, 34.366, 31.976
Angle α, β, γ (deg.)90.000, 127.500, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: C (n fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

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Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Mass: 3887.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium cacodylate, pH 6.0, 40 mM sodium chloride, 10 mM magnesium chloride, 6 mM spermine tetrahydrochloride, and 5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 11122 / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Rrim(I) all: 0.077 / Χ2: 1.854 / Net I/av σ(I): 44.679 / Net I/σ(I): 11.6 / Num. measured all: 62980
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.242.60.29310500.8750.2090.3610.75194
1.24-1.293.40.26611160.9110.1650.3140.87599.2
1.29-1.354.20.28810900.9510.150.3260.878100
1.35-1.425.60.31711320.9620.140.3470.927100
1.42-1.516.80.26911020.9740.1110.2911.13999.9
1.51-1.636.90.16411160.9880.0670.1771.592100
1.63-1.7970.1111300.9950.0450.1191.932100
1.79-2.056.90.08911150.9940.0370.0972.378100
2.05-2.596.70.07111210.9950.030.0772.915100
2.59-506.20.05311500.9950.0260.063.21699.6

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID:2Q1R

2q1r


Resolution: 1.2→50 Å / WRfactor Rfree: 0.2297 / WRfactor Rwork: 0.19 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 553 5 %Random
Rwork0.19 ---
obs-11102 99.3 %-
Displacement parametersBiso max: 152.45 Å2 / Biso mean: 19.0865 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 0 67 322

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