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Human Topoisomerase 2 Beta ATPase domain bound to obex 5c and non-hydrolyzable ATP analog AMPPNP
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 7 293 17% PEG3350, 0.1M potassium citrate, 0.1M HEPES pH7.0
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.148 α = 90 b = 84.148 β = 90 c = 127.752 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS EIGER X 16M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 1.45 50 99.9 0.047 0.05 0.018 0.999 10.5 7.4 81673
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) Redundancy Number Unique Reflections (All) 1 1.45 1.5 99.9 1.228 1.317 0.47 0.569 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 43.54 1.34 81098 2000 99.27 0.1562 0.1559 0.1577 0.1717 0.1731
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.964 f_angle_d 1.013 f_chiral_restr 0.08 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3107 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling DENZO data reduction PHENIX phasing