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- PDB-3s8u: Crystal structure of a 2-azido-adenine-modified RNA -

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Basic information

Entry
Database: PDB / ID: 3s8u
TitleCrystal structure of a 2-azido-adenine-modified RNA
ComponentsEcoli 23 S rRNA Sarcin Ricin loop
KeywordsRNA / hairpin RNA / RNA labelling / 2'-azido-adenine
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.2 Å resolution
AuthorsEnnifar, E. / Micura, R.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: 2'-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling.
Authors: Fauster, K. / Hartl, M. / Santner, T. / Aigner, M. / Kreutz, C. / Bister, K. / Ennifar, E. / Micura, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 31, 2011 / Release: Apr 11, 2012

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ecoli 23 S rRNA Sarcin Ricin loop


Theoretical massNumber of molelcules
Total (without water)8,7701
Polyers8,7701
Non-polymers00
Water2,918162
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)29.570, 29.570, 76.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP 43

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Components

#1: RNA chain Ecoli 23 S rRNA Sarcin Ricin loop


Mass: 8770.275 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Formula: H2O / Water

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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: 1.9 / Density percent sol: 35.36 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 volume of [3.1M (NH4)2SO4, 50mM MOPS pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes of [RNA in 1mM EDTA, 10mM Tris pH8.0], VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: May 9, 2011
RadiationMonochromator: crystal / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionD resolution high: 1.2 Å / D resolution low: 30 Å / Number all: 20495 / Number obs: 19989 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / Rmerge I obs: 0.114 / Percent possible obs: 97.5
Reflection shellRmerge I obs: 0.545 / Highest resolution: 1.2 Å / Lowest resolution: 1.23 Å / MeanI over sigI obs: 2.67 / Number unique all: 1549 / Percent possible all: 91.1

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DVZ
Overall SU ML: 0.13 / R Free selection details: RANDOM / Sigma F: 2.01 / Overall phase error: 15.68 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.41 Å / Solvent vdw probe radii: 0.6 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 59.085 / Solvent model param ksol: 0.456
Displacement parametersAniso B11: 1.6349 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 1.6349 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.4249 Å2
Least-squares processR factor R free: 0.1785 / R factor R work: 0.1428 / R factor obs: 0.1445 / Highest resolution: 1.2 Å / Lowest resolution: 27.574 Å / Number reflection R free: 1000 / Number reflection all: 20495 / Number reflection obs: 19980 / Percent reflection R free: 5.01 / Percent reflection obs: 97.67
Refine hist #LASTHighest resolution: 1.2 Å / Lowest resolution: 27.574 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 581 / Ligand: 0 / Solvent: 162 / Total: 743
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019707
X-RAY DIFFRACTIONf_angle_d1.7841106
X-RAY DIFFRACTIONf_dihedral_angle_d16.888348
X-RAY DIFFRACTIONf_chiral_restr0.100148
X-RAY DIFFRACTIONf_plane_restr0.03329
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.20010.21710.19081.2634137259394.00
1.26340.20970.15561.3425145275299.00
1.34250.18610.14291.4462143272399.00
1.44620.19980.12501.5917143272299.00
1.59170.16380.11451.8220145275199.00
1.82200.16950.13402.2954144272298.00
2.29540.17250.153027.5810143271797.00

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