8T80

Sequence specific (AATT) orientation of Hoechst 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 Na Cacodylate pH 6.0 with 200 mM MgCl2 and 2.5 M KCl was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Crystal Properties
Matthews coefficientSolvent content
6.2580.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.503α = 90
b = 68.503β = 90
c = 59.129γ = 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
12.95094.40.1220.130.0450.9817.38.26418
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)
12.92.9566.41.3481.4620.5530.6875.7

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 REPLACEMENTTHROUGHOUT2.9141.88593130591.920.220230.219360.23551RANDOM113.191
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]
-0.22-0.11-0.220.73
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined18.143
r_long_range_B_other18.137
r_scangle_other15.347
r_scbond_it10.652
r_scbond_other10.647
r_angle_refined_deg1.829
r_angle_other_deg0.512
r_chiral_restr0.151
r_gen_planes_refined0.012
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined18.143
r_long_range_B_other18.137
r_scangle_other15.347
r_scbond_it10.652
r_scbond_other10.647
r_angle_refined_deg1.829
r_angle_other_deg0.512
r_chiral_restr0.151
r_gen_planes_refined0.012
r_bond_other_d0.009
r_bond_refined_d0.006
r_gen_planes_other0.002
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 Atoms856
Solvent Atoms6
Heterogen Atoms69

Software

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