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- PDB-4hqh: Decamer Fluoro Carbocyclic LNA (R-F-cLNA) crystal structure -

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Basic information

Entry
Database: PDB / ID: 4hqh
TitleDecamer Fluoro Carbocyclic LNA (R-F-cLNA) crystal structure
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(ULF)P*AP*CP*GP*C)-3')
KeywordsDNA / A-form DNA / carbocyclic LNA / cLNA / R-F-cLNA
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOL REP CCP4 / Resolution: 1.8 Å
AuthorsSeth, P.P. / Pallan, P.S. / Swayze, E.E. / Egli, M.
CitationJournal: To be Published
Title: Properties of a Fluorinated Carbocyclic LNA Analog
Authors: Seth, P.P. / Pallan, P.S. / Swayze, E.E. / Egli, M.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(ULF)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(ULF)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1502
Polymers6,1502
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.115, 43.859, 45.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*(ULF)P*AP*CP*GP*C)-3')


Mass: 3075.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM sodium cacodylate, pH 7.0, 40 mM potassium chloride, 6 mM Sodium Chloride, 6 mM spermine tetrahydrochloride, and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0079 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 1.8→31.67 Å / Num. obs: 4674 / % possible obs: 97.3 % / Observed criterion σ(I): 5 / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.35
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.4 / Num. unique all: 244 / % possible all: 75.5

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
CCP4model building
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOL REP CCP4
Starting model: PDB ID 3EY2

3ey2


Resolution: 1.8→31.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.844 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.154 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24609 380 7.5 %RANDOM
Rwork0.19802 ---
obs0.20165 4674 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 68 476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.012458
X-RAY DIFFRACTIONr_angle_refined_deg2.6971.503704
X-RAY DIFFRACTIONr_chiral_restr0.1490.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02208
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 25 -
Rwork0.214 244 -
obs-244 75.77 %

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