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- PDB-4izq: GGGCATGCCC in the A-DNA Form -

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Basic information

Entry
Database: PDB / ID: 4izq
TitleGGGCATGCCC in the A-DNA Form
ComponentsDNA (5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')
KeywordsDNA / A-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHall, J.P. / Ruiz-Morte, S. / Murray, C.A. / Cardin, C.J.
CitationJournal: To be Published
Title: GGGCATGCCC in the A-DNA Form
Authors: Hall, J.P. / Ruiz-Morte, S. / Murray, C.A. / Cardin, C.J.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area3760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.820, 43.900, 46.570
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*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')


Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Purchased from ATDBio
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1mM 2-phenylpyridine-Pd12-cyanurate, 80mM KCl, 40mM Na-cacodylate, 20mM BaCl2, 12mM spermine, 10%(v/v) 2-methyl-2,4-pentanediol, 1ml 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, ...Details: 0.1mM 2-phenylpyridine-Pd12-cyanurate, 80mM KCl, 40mM Na-cacodylate, 20mM BaCl2, 12mM spermine, 10%(v/v) 2-methyl-2,4-pentanediol, 1ml 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2012
RadiationMonochromator: Si(111) dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.04→31.94 Å / Num. all: 3153 / Num. obs: 3153 / % possible obs: 90.7 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.04→2.09 Å / % possible all: 57.3

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal A-DNA from Coot

Resolution: 2.04→31.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.187 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 137 4.4 %RANDOM
Rwork0.19703 ---
obs0.1997 3001 89.33 %-
all-3301 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.844 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2--1.04 Å2-0 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.04→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 22 426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011452
X-RAY DIFFRACTIONr_bond_other_d0.0030.02224
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.157694
X-RAY DIFFRACTIONr_angle_other_deg1.4693528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 9 -
Rwork0.311 132 -
obs--55.08 %

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