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

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Basic information

Entry
Database: PDB / ID: 4rnk
TitleSequence and structure of a self-assembled 3-D DNA crystal: D(GGAAAATTTGGAG)
ComponentsGGAAAATTTGGAG
KeywordsDNA / 3D DNA Lattice
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSaoji, M.M. / Paukstelis, P.J.
CitationJournal: 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.
History
DepositionOct 24, 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 ...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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: GGAAAATTTGGAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1283
Polymers4,0801
Non-polymers492
Water1629
1
A: GGAAAATTTGGAG
hetero molecules

A: GGAAAATTTGGAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2576
Polymers8,1592
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)39.729, 39.729, 55.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

DetailsThis DNA monomer self assembles in presence of divalent cations to form 3D DNA crystals.

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Components

#1: DNA chain GGAAAATTTGGAG


Mass: 4079.684 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The DNA sample was synthesized using a DNA synthesizer.
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
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: 2.08→55.99 Å / Num. obs: 3045 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.4
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / Num. unique all: 426

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P1Y

1p1y


Resolution: 2.08→34.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.485 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 280 9.3 %RANDOM
Rwork0.20098 ---
obs0.20444 2738 98.76 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å2-0 Å2
2--0.3 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.08→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 2 9 265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011286
X-RAY DIFFRACTIONr_bond_other_d0.0020.02136
X-RAY DIFFRACTIONr_angle_refined_deg1.81.161442
X-RAY DIFFRACTIONr_angle_other_deg1.8763322
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_restr0.0810.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02149
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0258
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_it2.5323.306286
X-RAY DIFFRACTIONr_scbond_other2.4553.281284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7514.958440
X-RAY DIFFRACTIONr_long_range_B_refined4.79231.963412
X-RAY DIFFRACTIONr_long_range_B_other4.73331.864412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.078→2.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 16 -
Rwork0.324 182 -
obs--92.09 %
Refinement TLS params.Method: refined / Origin x: 10.68 Å / Origin y: -14.636 Å / Origin z: -12.052 Å
111213212223313233
T0.2322 Å2-0.0626 Å2-0.012 Å2-0.2664 Å2-0.0098 Å2--0.1286 Å2
L2.4826 °21.4319 °2-3.6089 °2-4.9095 °2-1.5752 °2--8.5146 °2
S-0.4915 Å °-0.1216 Å °-0.1326 Å °-0.8345 Å °0.19 Å °-0.2823 Å °0.5049 Å °-0.2031 Å °0.3015 Å °

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