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- PDB-4roo: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGA... -

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Basic information

Entry
Database: PDB / ID: 4roo
TitleSequence and structure of a self-assembled 3-D DNA crystal: D(GGACCGCGGGGAG)
ComponentsD(GGACCGCGGGGAG)
KeywordsDNA / Self-assembling 3D DNA crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsSaoji, M.M. / Paukstelis, P.J.
Citation
Journal: Biopolymers / Year: 2015
Title: Probing the role of sequence in the assembly of three-dimensional DNA crystals.
Authors: Saoji, M. / Zhang, D. / Paukstelis, P.J.
#1: Journal: Chem.Biol. / Year: 2004
Title: Crystal structure of a continuous three-dimensional DNA lattice.
Authors: Paukstelis, P.J. / Nowakowski, J. / Birktoft, J.J. / Seeman, N.C.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: D(GGACCGCGGGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1072
Polymers4,0831
Non-polymers241
Water00
1
A: D(GGACCGCGGGGAG)
hetero molecules

A: D(GGACCGCGGGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2144
Polymers8,1652
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)40.789, 40.789, 52.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: DNA chain D(GGACCGCGGGGAG)


Mass: 4082.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA molecule synthesized using a DNA synthesizer.
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K
PH range: none

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.37→52.01 Å / Num. obs: 1999 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 23
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.257 / Mean I/σ(I) obs: 0.9 / Num. unique all: 291

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p1y

1p1y


Resolution: 2.37→35.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.893 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30136 181 9.3 %RANDOM
Rwork0.2373 ---
obs0.24356 1772 96.44 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.754 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0.56 Å2-0 Å2
2---1.12 Å20 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.37→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 1 0 255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011286
X-RAY DIFFRACTIONr_bond_other_d0.0030.02133
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.144442
X-RAY DIFFRACTIONr_angle_other_deg1.6643313
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_restr0.080.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02155
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0270
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7498.531286
X-RAY DIFFRACTIONr_scbond_other5.7238.498284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.26212.806439
X-RAY DIFFRACTIONr_long_range_B_refined12.26982.365428
X-RAY DIFFRACTIONr_long_range_B_other12.25582.314429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.373→2.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.894 13 -
Rwork0.011 128 -
obs--95.27 %

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