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- PDB-1r3o: Crystal structure of the first RNA duplex in L-conformation at 1.... -

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Basic information

Entry
Database: PDB / ID: 1r3o
TitleCrystal structure of the first RNA duplex in L-conformation at 1.9A resolution
Components(L-RNA) x 2
KeywordsRNA / L-RNA
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVallazza, M. / Perbandt, M. / Klussmann, S. / Rypniewski, W. / Erdmann, V.A. / Betzel, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: First look at RNA in L-configuration.
Authors: Vallazza, M. / Perbandt, M. / Klussmann, S. / Rypniewski, W. / Einspahr, H.M. / Erdmann, V.A. / Betzel, C.h.
History
DepositionOct 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-RNA
B: L-RNA
C: L-RNA
D: L-RNA


Theoretical massNumber of molelcules
Total (without water)10,2304
Polymers10,2304
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.109, 46.109, 263.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-8-

HOH

21A-12-

HOH

31A-64-

HOH

41C-92-

HOH

51C-102-

HOH

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Components

#1: RNA chain L-RNA


Mass: 2597.601 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain L-RNA


Mass: 2517.553 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growpH: 7 / Details: pH 7.0, temperature 100K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 %(v/v)MPD1drop
280 mM1dropKCl
320 mM1dropBaCl2
412 mMspermine tetrahydrochloride1drop
540 mMsodium cacodylate1droppH6.0
60.25 mMRNA1drop
730 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20.54 Å / Num. obs: 8385 / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.065
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 8949 / % possible obs: 98.7 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 98.9 % / Num. unique obs: 511 / Rmerge(I) obs: 0.47

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.399 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28563 388 4.6 %RANDOM
Rwork0.23855 ---
obs0.24082 7996 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 676 0 129 805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021752
X-RAY DIFFRACTIONr_bond_other_d0.0020.02260
X-RAY DIFFRACTIONr_angle_refined_deg1.76631168
X-RAY DIFFRACTIONr_angle_other_deg1.3433680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr5.1080.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.0980.251
X-RAY DIFFRACTIONr_nbd_other0.2110.2321
X-RAY DIFFRACTIONr_nbtor_other0.0550.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0530.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.120.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.7463752
X-RAY DIFFRACTIONr_scangle_it2.334.51168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.413 33
Rwork0.292 511
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS

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