8KGT

Structure of African swine fever virus topoisomerase II in complex with dsDNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldModel generated by AlphaFold2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.1521% PEG 3350, 100 mM Hepes (pH 7.2) and 200 mM Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.234α = 90
b = 85.234β = 90
c = 209.809γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2022-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.35099.40.0940.1590.0550.99914.228.220799
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3499.40.9450.6292.247.7

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 REPLACEMENTTHROUGHOUT2.342.791979398899.560.195590.193140.24593RANDOM42.263
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]
0.610.310.61-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.375
r_dihedral_angle_2_deg7.408
r_long_range_B_refined7.137
r_long_range_B_other7.127
r_dihedral_angle_1_deg6.59
r_scangle_other5.063
r_mcangle_it4.227
r_mcangle_other4.225
r_scbond_it3.13
r_scbond_other3.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.375
r_dihedral_angle_2_deg7.408
r_long_range_B_refined7.137
r_long_range_B_other7.127
r_dihedral_angle_1_deg6.59
r_scangle_other5.063
r_mcangle_it4.227
r_mcangle_other4.225
r_scbond_it3.13
r_scbond_other3.13
r_mcbond_it2.684
r_mcbond_other2.683
r_angle_refined_deg1.135
r_angle_other_deg0.383
r_chiral_restr0.055
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3080
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms27

Software

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