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- PDB-6y0t: Sarcin Ricin Loop, mutant C2666A U2653G C2667A -

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Basic information

Entry
Database: PDB / ID: 6y0t
TitleSarcin Ricin Loop, mutant C2666A U2653G C2667A
ComponentsRNA (27-MER)
KeywordsRNA / ribosome
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.393 Å
AuthorsEnnifar, E. / Westhof, E.
CitationJournal: To Be Published
Title: Sarcin Ricin Loop, mutant C2666A U2653G C2667A
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 (27-MER)
B: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,95511
Polymers17,6632
Non-polymers2939
Water5,080282
1
A: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9976
Polymers8,8311
Non-polymers1665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9585
Polymers8,8311
Non-polymers1274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.170, 23.960, 63.820
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (27-MER)


Mass: 8831.344 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 80mM KCl, 20mM MgCl2, 40mM Na cacodylate pH 6.0, 46% MPD, 12mM spermine tetrahydrochloride

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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: 1.39→33.72 Å / Num. obs: 30750 / % possible obs: 98.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 15.4
Reflection shellResolution: 1.39→1.43 Å / Num. unique obs: 1911 / CC1/2: 0.419

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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: 1.393→33.72 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2028 1534 5 %
Rwork0.1657 --
obs0.1675 30660 98.58 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å
Refinement stepCycle: LAST / Resolution: 1.393→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1172 9 282 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061450
X-RAY DIFFRACTIONf_angle_d1.2152264
X-RAY DIFFRACTIONf_dihedral_angle_d12.444710
X-RAY DIFFRACTIONf_chiral_restr0.05296
X-RAY DIFFRACTIONf_plane_restr0.01460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3933-1.43830.38481180.32762233X-RAY DIFFRACTION85
1.4383-1.48970.30351410.26722675X-RAY DIFFRACTION100
1.4897-1.54930.2841380.23022633X-RAY DIFFRACTION100
1.5493-1.61980.22131410.18252668X-RAY DIFFRACTION100
1.6198-1.70520.22221400.15892672X-RAY DIFFRACTION100
1.7052-1.8120.16031400.14462651X-RAY DIFFRACTION100
1.812-1.95190.17651410.1422677X-RAY DIFFRACTION100
1.9519-2.14830.19361410.14682683X-RAY DIFFRACTION100
2.1483-2.45910.19411420.15942696X-RAY DIFFRACTION100
2.4591-3.09790.19621430.15872728X-RAY DIFFRACTION100
3.0979-100.19191490.15922810X-RAY DIFFRACTION100

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