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Human Topoisomerase II Beta ATPase ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium sulphate, 0.1 M bis tris (pH 5.5), 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.4 α = 90 b = 103.4 β = 90 c = 67.02 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99987 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 53.714 99.8 0.996 11 19.2 18666
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.565 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QFO 2.3 53.714 18661 983 99.727 0.201 0.1972 0.1971 0.2593 0.2595 43.233
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] 0.456 0.228 0.456 -1.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.198 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_6_deg 15.43 r_lrange_it 10.59 r_lrange_other 10.554 r_dihedral_angle_1_deg 8.326 r_scangle_it 8.108 r_scangle_other 8.106 r_mcangle_it 6.393 r_mcangle_other 6.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.198 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_6_deg 15.43 r_lrange_it 10.59 r_lrange_other 10.554 r_dihedral_angle_1_deg 8.326 r_scangle_it 8.108 r_scangle_other 8.106 r_mcangle_it 6.393 r_mcangle_other 6.392 r_scbond_it 5.763 r_scbond_other 5.761 r_mcbond_it 4.542 r_mcbond_other 4.527 r_angle_refined_deg 1.82 r_angle_other_deg 0.587 r_symmetry_nbd_refined 0.295 r_nbd_refined 0.231 r_symmetry_nbd_other 0.198 r_nbd_other 0.192 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.083 r_metal_ion_refined 0.063 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_chiral_restr_other 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2909 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Coot model building MolProbity model building pointless data scaling Aimless data scaling MOLREP phasing