8T7X

Sequence specific (AATT) orientation of DAPI molecules at two unique minor groove binding sites within a self-assembled 3D DNA lattice (4x5)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KEK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.5 mL of 0.05 M Cacodylate pH 6.0 with 18 mM MgCl2, 2.25 mM spermine, 1 mM CuSO4, and 9% Isopropanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Crystal Properties
Matthews coefficientSolvent content
6.3680.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.479α = 90
b = 68.479β = 90
c = 60.082γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.92ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
13.055099.90.0890.0940.030.91210.3105900
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.11000.8630.9150.2990.9469.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE3.0742.212.02577528197.570.19820.1970.2218
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_d34.939
f_angle_d1.088
f_chiral_restr0.068
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms855
Solvent Atoms
Heterogen Atoms43

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing