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

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Basic information

Entry
Database: PDB / ID: 4roy
TitleSequence and structure of a self-assembled 3-D DNA crystal: D(GGACGATCGGGAG)
ComponentsD(GGACGATCGGGAG)
KeywordsDNA / Self-assembling 3D DNA crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 29, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(GGACGATCGGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1062
Polymers4,0821
Non-polymers241
Water724
1
A: D(GGACGATCGGGAG)
hetero molecules

A: D(GGACGATCGGGAG)
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)40.442, 40.442, 52.514
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(GGACGATCGGGAG)


Mass: 4081.660 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
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: 2.09→35.02 Å / Num. obs: 2944 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 33.6
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.8 / Num. unique all: 421

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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: 2.09→35.02 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 15.015 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25032 272 9.3 %RANDOM
Rwork0.22167 ---
obs0.22437 2655 99.19 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å2-0 Å2
2--0.48 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.09→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 1 4 259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.011286
X-RAY DIFFRACTIONr_bond_other_d0.0020.02134
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.15442
X-RAY DIFFRACTIONr_angle_other_deg1.5633316
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_restr0.0660.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0266
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_it3.0853.255286
X-RAY DIFFRACTIONr_scbond_other3.0833.227284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.134.889440
X-RAY DIFFRACTIONr_long_range_B_refined6.13329.443412
X-RAY DIFFRACTIONr_long_range_B_other6.12529.42413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 19 -
Rwork0.452 204 -
obs--97.81 %
Refinement TLS params.Method: refined / Origin x: 10.999 Å / Origin y: -14.793 Å / Origin z: -12.083 Å
111213212223313233
T0.3378 Å2-0.1433 Å2-0.0847 Å2-0.4192 Å2-0.0211 Å2--0.2891 Å2
L4.113 °21.5752 °2-4.7354 °2-8.4396 °2-4.3814 °2--11.3433 °2
S-0.516 Å °-0.011 Å °-0.2255 Å °-1.3156 Å °0.2553 Å °-0.2777 Å °0.8615 Å °-0.3357 Å °0.2607 Å °

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