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Structure of African swine fever virus topoisomerase II in complex with dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Model generated by AlphaFold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 21% PEG 3350, 100 mM Hepes (pH 7.2) and 200 mM Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.2 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.234 α = 90 b = 85.234 β = 90 c = 209.809 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 50 99.4 0.094 0.159 0.055 0.999 14.22 8.2 20799
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) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99.4 0.945 0.629 2.24 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 42.79 19793 988 99.56 0.19559 0.19314 0.2048 0.24593 0.2388 RANDOM 42.263
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] 0.61 0.31 0.61 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.375 r_dihedral_angle_2_deg 7.408 r_long_range_B_refined 7.137 r_long_range_B_other 7.127 r_dihedral_angle_1_deg 6.59 r_scangle_other 5.063 r_mcangle_it 4.227 r_mcangle_other 4.225 r_scbond_it 3.13 r_scbond_other 3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.375 r_dihedral_angle_2_deg 7.408 r_long_range_B_refined 7.137 r_long_range_B_other 7.127 r_dihedral_angle_1_deg 6.59 r_scangle_other 5.063 r_mcangle_it 4.227 r_mcangle_other 4.225 r_scbond_it 3.13 r_scbond_other 3.13 r_mcbond_it 2.684 r_mcbond_other 2.683 r_angle_refined_deg 1.135 r_angle_other_deg 0.383 r_chiral_restr 0.055 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3080 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing