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- PDB-6y0y: Sarcin Ricin Loop, mutant C2666U -

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Basic information

Entry
Database: PDB / ID: 6y0y
TitleSarcin Ricin Loop, mutant C2666U
ComponentsRNA (27-MER)
KeywordsRNA / ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsEnnifar, E. / Westhof, E.
CitationJournal: To Be Published
Title: Sarcin Ricin Loop, mutant C2666U
Authors: Ennifar, E. / Westhof, E.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8163
Polymers8,7681
Non-polymers472
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area4780 Å2
Unit cell
Length a, b, c (Å)22.480, 27.550, 29.690
Angle α, β, γ (deg.)91.58, 93.61, 108.31
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain RNA (27-MER)


Mass: 8768.279 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 5mM MgCl2, 50mM Na HEPES pH 7.0, 25% PEG-MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 0.89→35 Å / Num. obs: 47148 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 13.27
Reflection shellResolution: 0.89→0.92 Å / Num. unique obs: 2093 / CC1/2: 0.263

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 0.95→21.281 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 15.92
RfactorNum. reflection% reflection
Rfree0.1387 1731 5 %
Rwork0.1252 --
obs0.1259 34635 81.49 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å
Refinement stepCycle: LAST / Resolution: 0.95→21.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 581 2 179 762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007651
X-RAY DIFFRACTIONf_angle_d1.2661015
X-RAY DIFFRACTIONf_dihedral_angle_d12.369320
X-RAY DIFFRACTIONf_chiral_restr0.052134
X-RAY DIFFRACTIONf_plane_restr0.01927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.9780.3276590.36561119X-RAY DIFFRACTION33
0.978-1.00950.2819800.29271520X-RAY DIFFRACTION46
1.0095-1.04560.27441180.23092249X-RAY DIFFRACTION67
1.0456-1.08750.18261460.17252768X-RAY DIFFRACTION82
1.0875-1.1370.15481550.13952948X-RAY DIFFRACTION87
1.137-1.19690.14361600.1173075X-RAY DIFFRACTION92
1.1969-1.27190.10741650.10993144X-RAY DIFFRACTION94
1.2719-1.37010.15121690.11133212X-RAY DIFFRACTION95
1.3701-1.50790.11611700.11163226X-RAY DIFFRACTION95
1.5079-1.7260.11821690.10963211X-RAY DIFFRACTION95
1.726-2.17430.13441690.11913206X-RAY DIFFRACTION96
2.1743-100.13451710.12183226X-RAY DIFFRACTION96

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