8TB4

Sequence specific (AATT) orientation of DAPI molecules at a unique minor groove binding site (position2) 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 HEPES pH 7.5 with 15 mM MgCl2, 1.0 mM spermidine, and 10% dioxan was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Crystal Properties
Matthews coefficientSolvent content
6.4981.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.507α = 90
b = 69.507β = 90
c = 59.552γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.92APS19-ID

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
13.15099.70.1290.1360.04216.19.75774
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)
13.13.1597.31.6291.7550.6270.6446.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.1142.37533530497.120.197280.195010.23789RANDOM138.397
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]
0.020.010.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined24.044
r_long_range_B_other24.037
r_scangle_other19.044
r_scbond_it14.663
r_scbond_other14.656
r_angle_refined_deg2.066
r_angle_other_deg1.647
r_chiral_restr0.146
r_bond_other_d0.068
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined24.044
r_long_range_B_other24.037
r_scangle_other19.044
r_scbond_it14.663
r_scbond_other14.656
r_angle_refined_deg2.066
r_angle_other_deg1.647
r_chiral_restr0.146
r_bond_other_d0.068
r_gen_planes_refined0.011
r_bond_refined_d0.006
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms855
Solvent Atoms
Heterogen Atoms24

Software

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