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- PDB-3s7c: Crystal structure of a 2'-azido-uridine-modified RNA -

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Basic information

Entry
Database: PDB / ID: 3s7c
TitleCrystal structure of a 2'-azido-uridine-modified RNA
ComponentsEcoli 23 S rRNA Sarcin Ricin loop
KeywordsRNA / hairpin RNA / RNA labelling / 2'-azido-uridine
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.1 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 26, 2011 / Release: Apr 11, 2012
RevisionDateData content typeGroupCategoryProviderType
1.0Apr 11, 2012Structure modelrepositoryInitial release
1.1Nov 29, 2017Structure modelDatabase referencespdbx_database_related

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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
Water3,567198
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)29.610, 29.610, 76.180
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 35.4 %
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 NaEDTA, 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
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionD resolution high: 1.1 Å / D resolution low: 50 Å / Number all: 26603 / Number obs: 26490 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Percent possible obs: 99.6
Reflection shellRmerge I obs: 0.454 / Highest resolution: 1.1 Å / Lowest resolution: 1.13 Å / MeanI over sigI obs: 2.91 / Percent possible all: 94.3

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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
Sigma F: 2.06 / Overall phase error: 20.9 / Stereochemistry target values: TWIN_LSQ_F
Solvent computationSolvent shrinkage radii: 0.47 Å / Solvent vdw probe radii: 0.8 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 82.04 / Solvent model param ksol: 0.435
Displacement parametersAniso B11: 0.5863 Å2 / Aniso B12: 0 Å2 / Aniso B13: - Å2 / Aniso B22: 0.5863 Å2 / Aniso B23: - Å2 / Aniso B33: -1.1725 Å2
Least-squares processR factor R free: 0.1559 / R factor R work: 0.1166 / R factor obs: 0.118 / Highest resolution: 1.1 Å / Lowest resolution: 29.61 Å / Number reflection R free: 1326 / Number reflection all: 26477 / Number reflection obs: 26483 / Percent reflection R free: 5.01 / Percent reflection obs: 99.8
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refine hist #LASTHighest resolution: 1.1 Å / Lowest resolution: 29.61 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 581 / Ligand: 0 / Solvent: 198 / Total: 779
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005707
X-RAY DIFFRACTIONf_angle_d0.9691106
X-RAY DIFFRACTIONf_dihedral_angle_d17.137350
X-RAY DIFFRACTIONf_chiral_restr0.063146
X-RAY DIFFRACTIONf_plane_restr0.01029
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
1.10020.24630.21411.1442144273393.00
1.14420.22630.20111.1963147278795.00
1.19630.18600.17741.2594147279895.00
1.25940.18370.16451.3383148280595.00
1.33830.17240.16441.4416147280595.00
1.44160.16980.15491.5867146277195.00
1.58670.13650.12541.8162148281395.00
1.81620.15320.11452.2881149281995.00
2.28810.13950.067927.6072149282695.00

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