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- PDB-3jxq: X-Ray structure of r[CGCG(5-fluoro)CG]2 -

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Basic information

Entry
Database: PDB / ID: 3jxq
TitleX-Ray structure of r[CGCG(5-fluoro)CG]2
Componentsr[CGCG(5-fluoro)CG]2
KeywordsRNA / double helix
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAdamiak, D.A. / Milecki, J. / Adamiak, R.W. / Rypniewski, W.
CitationJournal: New J.Chem. / Year: 2010
Title: The hydration and unusual hydrogen bonding in the crystal structure of an RNA duplex containing alternating CG base pairs
Authors: Adamiak, D.A. / Milecki, J. / Adamiak, R.W. / Rypniewski, W.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: r[CGCG(5-fluoro)CG]2
B: r[CGCG(5-fluoro)CG]2
K: r[CGCG(5-fluoro)CG]2
L: r[CGCG(5-fluoro)CG]2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7948
Polymers7,6974
Non-polymers974
Water2,378132
1
A: r[CGCG(5-fluoro)CG]2
B: r[CGCG(5-fluoro)CG]2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8974
Polymers3,8482
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: r[CGCG(5-fluoro)CG]2
L: r[CGCG(5-fluoro)CG]2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8974
Polymers3,8482
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.224, 26.486, 29.310
Angle α, β, γ (deg.)97.56, 105.47, 109.38
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain
r[CGCG(5-fluoro)CG]2


Mass: 1924.195 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: This is a modification of a naturally occuring sequence
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M lithium sulfate, 10mM magnesium chloride and 50mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2001 / Details: Si(111)
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 9439 / Num. obs: 9439 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.041 / Net I/σ(I): 30
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 409 / Rsym value: 0.296 / % possible all: 80

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.655 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20517 174 1.9 %RANDOM
Rwork0.17115 ---
all0.17181 ---
obs0.17181 9199 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.41 Å2-0.32 Å2
2---0.47 Å2-0.74 Å2
3---0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.079 Å-
Luzzati sigma a-0.059 Å
Refinement stepCycle: LAST / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 508 4 132 644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021567
X-RAY DIFFRACTIONr_angle_refined_deg2.0223870
X-RAY DIFFRACTIONr_chiral_restr0.0780.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02252
X-RAY DIFFRACTIONr_nbd_refined0.1760.2195
X-RAY DIFFRACTIONr_nbtor_refined0.2760.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.292
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.218
X-RAY DIFFRACTIONr_scbond_it2.4797827
X-RAY DIFFRACTIONr_scangle_it3.0989870
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 13 -
Rwork0.259 596 -
obs-596 100 %

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