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Human Topoisomerase II Beta ATPase ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 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 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.021 α = 90 b = 103.021 β = 90 c = 66.693 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 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 Diamond I03
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 2.62 89.22 100 0.997 9 10.8 12596
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 2.62 2.74 100 0.78 1.7 11
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 D_1292119290 2.621 89.219 12583 540 99.929 0.202 0.1993 0.1992 0.2588 0.2588 60.189
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] 1.796 0.898 1.796 -5.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.251 r_dihedral_angle_6_deg 16.099 r_dihedral_angle_2_deg 9.812 r_lrange_it 9.424 r_lrange_other 9.423 r_dihedral_angle_1_deg 9.256 r_scangle_it 7.576 r_scangle_other 7.557 r_mcangle_other 6.243 r_mcangle_it 6.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.251 r_dihedral_angle_6_deg 16.099 r_dihedral_angle_2_deg 9.812 r_lrange_it 9.424 r_lrange_other 9.423 r_dihedral_angle_1_deg 9.256 r_scangle_it 7.576 r_scangle_other 7.557 r_mcangle_other 6.243 r_mcangle_it 6.242 r_scbond_it 5.215 r_scbond_other 5.179 r_mcbond_it 4.398 r_mcbond_other 4.396 r_angle_refined_deg 1.935 r_angle_other_deg 0.641 r_symmetry_xyhbond_nbd_refined 0.358 r_nbd_refined 0.236 r_symmetry_nbd_other 0.206 r_nbd_other 0.19 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_metal_ion_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2886 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction MolProbity model building pointless data scaling Coot model building Aimless data scaling PHASER phasing MOLREP phasing