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- PDB-3ot0: Crystal structure of a DNA containing the rigid nitroxide spin-la... -

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Basic information

Entry
Database: PDB / ID: 3ot0
TitleCrystal structure of a DNA containing the rigid nitroxide spin-labeled nucleotide C-spin
ComponentsSpin-labeled DNA
KeywordsDNA / nitroxide / spin-label / EPR spectroscopy / fluorescence spectroscopy / modified nucleic acid / C-spin / deoxycytosine analog / phenoxazine / spectroscopic probe / PELDOR / 2'-O-methyl U
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7004 Å
AuthorsEdwards, T.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
Authors: Edwards, T.E. / Cekan, P. / Reginsson, G.W. / Shelke, S.A. / Ferre-D'Amare, A.R. / Schiemann, O. / Sigurdsson, S.T.
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 22, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _chem_comp.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: 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: Spin-labeled DNA
B: Spin-labeled DNA


Theoretical massNumber of molelcules
Total (without water)6,5262
Polymers6,5262
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.710, 44.550, 45.940
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/RNA hybrid Spin-labeled DNA


Mass: 3263.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, ...Details: 1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 17, 2010 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 5955 / Num. obs: 5613 / % possible obs: 94.3 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.022 / Net I/σ(I): 53.95
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.7-1.746.40.0720.03427182.9
1.74-1.790.06622.09415183.9
1.79-1.840.06224.02408186.8
1.84-1.90.05924.38397189.4
1.9-1.960.05129.14383192.7
1.96-2.030.04434.12374193.6
2.03-2.110.04136.44363195.6
2.11-2.190.04237.82351196.9
2.19-2.290.03446.96332198.2
2.29-2.40.0352.62315198.1
2.4-2.530.03158.44311199
2.53-2.690.0364.15294198.3
2.69-2.870.02671.03277198.6
2.87-3.10.02183.74263199.6
3.1-3.40.018102.89238198.7
3.4-3.80.018111.582141100
3.8-4.390.017115.451981100
4.39-5.380.019111.511701100
5.38-7.60.02108.161391100
7.6-500.02100.41861100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGK

1kgk


Resolution: 1.7004→16.824 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 533 9.54 %
Rwork0.1594 --
obs0.1632 5586 93.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.023 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0439 Å2-0 Å20 Å2
2---0.3863 Å2-0 Å2
3---0.4302 Å2
Refinement stepCycle: LAST / Resolution: 1.7004→16.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 436 0 83 519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007490
X-RAY DIFFRACTIONf_angle_d1.738762
X-RAY DIFFRACTIONf_dihedral_angle_d25.722208
X-RAY DIFFRACTIONf_chiral_restr0.06780
X-RAY DIFFRACTIONf_plane_restr0.00722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.87130.21821160.1381105X-RAY DIFFRACTION85
1.8713-2.14160.23421170.15841253X-RAY DIFFRACTION94
2.1416-2.69640.21861520.1771290X-RAY DIFFRACTION98
2.6964-16.82460.17281480.15571405X-RAY DIFFRACTION99

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