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- PDB-6zyb: Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification -

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Basic information

Entry
Database: PDB / ID: 6zyb
TitleSarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification
ComponentsSarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification
KeywordsRNA / Ribosome / modification
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsEnnifar, E.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundP27947 Austria
Austrian Science FundP31691 Austria
Austrian Research Promotion AgencyWest Austrian BioNMR 858017 Austria
CitationJournal: Chem Sci / Year: 2020
Title: 2'- O -Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy.
Authors: Himmelstoss, M. / Erharter, K. / Renard, E. / Ennifar, E. / Kreutz, C. / Micura, R.
History
DepositionJul 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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: Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification


Theoretical massNumber of molelcules
Total (without water)8,7961
Polymers8,7961
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.500, 29.500, 77.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: RNA chain Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification


Mass: 8796.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.9 Å3/Da / Density % sol: 35.27 % / Description: platelet
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2 M ammonium sulfate, 50 mM potassium MOPS, pH 7.0, 10 mM magnesium chloride, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.9→35 Å / Num. obs: 96381 / % possible obs: 100 % / Redundancy: 39.1 % / Biso Wilson estimate: 11.06 Å2 / CC1/2: 1 / Net I/σ(I): 45
Reflection shellResolution: 0.9→0.92 Å / Num. unique obs: 3626 / CC1/2: 0.555

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 0.9→29.5 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 18.221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1494 4824 5.01 %
Rwork0.131 91557 -
obs0.1319 96381 99.96 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.49 Å2
Refinement stepCycle: LAST / Resolution: 0.9→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 583 0 146 729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067741
X-RAY DIFFRACTIONf_angle_d1.55171156
X-RAY DIFFRACTIONf_chiral_restr0.0552151
X-RAY DIFFRACTIONf_plane_restr0.026232
X-RAY DIFFRACTIONf_dihedral_angle_d11.6719361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.910.39111580.37653009X-RAY DIFFRACTION99.81
0.91-0.920.36531650.34823110X-RAY DIFFRACTION99.97
0.92-0.930.31081590.31923014X-RAY DIFFRACTION99.75
0.93-0.940.26721610.29143059X-RAY DIFFRACTION99.88
0.94-0.960.28791600.27833048X-RAY DIFFRACTION100
0.96-0.970.31631610.25683037X-RAY DIFFRACTION100
0.97-0.980.27141650.25363128X-RAY DIFFRACTION99.94
0.98-10.30411560.24493007X-RAY DIFFRACTION100
1-1.010.19551620.18923066X-RAY DIFFRACTION100
1.01-1.030.24131610.19363036X-RAY DIFFRACTION100
1.03-1.050.18171610.17753054X-RAY DIFFRACTION99.94
1.05-1.070.17291600.16133060X-RAY DIFFRACTION99.84
1.07-1.090.16241590.15423013X-RAY DIFFRACTION99.94
1.09-1.110.18751600.15213056X-RAY DIFFRACTION100
1.11-1.130.16761620.13973094X-RAY DIFFRACTION100
1.13-1.160.15791590.14163011X-RAY DIFFRACTION100
1.16-1.190.16511610.13653072X-RAY DIFFRACTION99.94
1.19-1.220.13981620.12933078X-RAY DIFFRACTION100
1.22-1.260.15281560.1312998X-RAY DIFFRACTION99.94
1.26-1.30.13471630.13233086X-RAY DIFFRACTION99.94
1.3-1.340.14531630.13533083X-RAY DIFFRACTION100
1.34-1.40.17131620.12963059X-RAY DIFFRACTION100
1.4-1.460.14771590.1313010X-RAY DIFFRACTION100
1.46-1.540.1441630.12613063X-RAY DIFFRACTION100
1.54-1.640.12951590.11513053X-RAY DIFFRACTION100
1.64-1.760.121580.10733027X-RAY DIFFRACTION100
1.76-1.940.10481640.11463074X-RAY DIFFRACTION100
1.94-2.220.15261600.13173043X-RAY DIFFRACTION100
2.22-2.80.15931620.12943053X-RAY DIFFRACTION100
2.8-29.50.13211630.11063056X-RAY DIFFRACTION100

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