8CYM

[2T7+9bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle with 9 bp Sticky-End Linker


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7R96 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA
Crystal Properties
Matthews coefficientSolvent content
21.1694.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.13α = 90
b = 173.13β = 90
c = 87.833γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2021-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00743APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
17.7686.578715.19.81347186.16
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
17.768.840.389

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7R967.7649.981.3413346373.70.08080.07940.113635.74
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d39.4779
f_angle_d1.0008
f_chiral_restr0.0591
f_bond_d0.0089
f_plane_restr0.0062
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1218
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing