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

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Basic information

Entry
Database: PDB / ID: 4ron
TitleSequence and structure of a self-assembled 3-D DNA crystal: D(GGACCATGGGGAG)
ComponentsD(GGACCATGGGGAG)
KeywordsDNA / Self-assembling 3D DNA crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 ...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: D(GGACCATGGGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1062
Polymers4,0821
Non-polymers241
Water362
1
A: D(GGACCATGGGGAG)
hetero molecules

A: D(GGACCATGGGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2124
Polymers8,1632
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)40.719, 40.719, 51.214
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(GGACCATGGGGAG)


Mass: 4081.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA molecule synthesized on a DNA synthesizer
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 Å3/Da / Density % sol: 59.04 %
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: 2.39→51.21 Å / Num. obs: 1953 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.1
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.8 / Num. unique all: 289

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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: 2.39→35.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 28.05 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25245 183 9.5 %RANDOM
Rwork0.21082 ---
obs0.21499 1743 98.82 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.39→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 1 2 257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011286
X-RAY DIFFRACTIONr_bond_other_d0.0020.02134
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.15442
X-RAY DIFFRACTIONr_angle_other_deg1.7073316
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_restr0.0950.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0266
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_it3.3495.46285
X-RAY DIFFRACTIONr_scbond_other3.3475.434283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7688.207440
X-RAY DIFFRACTIONr_long_range_B_refined7.51451.984419
X-RAY DIFFRACTIONr_long_range_B_other7.46751.749418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.642 11 -
Rwork0.527 128 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.161 Å / Origin y: -14.788 Å / Origin z: -12.059 Å
111213212223313233
T0.2392 Å2-0.142 Å2-0.0132 Å2-0.2147 Å2-0.0078 Å2--0.2357 Å2
L1.6033 °21.5381 °2-0.7917 °2-3.2646 °2-1.9668 °2--9.6509 °2
S-0.4717 Å °-0.0064 Å °-0.0158 Å °-0.8702 Å °0.6133 Å °-0.0295 Å °0.6205 Å °-0.37 Å °-0.1415 Å °

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