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Crystal structure of the ATPase and transducer domains of DNA topoisomerase II from Balamuthia mandrillaris CDC:V039: baboon/San Diego/1986
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZXM PDB entry 1ZXM (as per MoRDa)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 18 mg/mL BamaA.19955.b.B2.PW38788 in Microlytics MCSG1 screen, condition a1 (20% w/v PEG2000, 100 mM HEPES free acid / NaOH, pH 7.5) + 3 mM magnesium chloride/AMPPNP, tray 315297 a1, cryoprotectant: 20% ethylene glycol + magnesium chloride/AMPPNP, puck cgp8-1
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.77 α = 90 b = 187.25 β = 90 c = 61.69 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 BERYIILUM LENSES 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 50 100 0.052 0.056 0.999 21.19 6.719 37513 39.655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.595 0.645 0.914 3.3 6.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 1ZXM (as per MoRDa) 1.95 39.74 1.34 37503 2066 99.96 0.1686 0.1671 0.1683 0.1958 0.1975 0 42.35
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 12.9564 f_angle_d 0.8001 f_chiral_restr 0.0552 f_bond_d 0.0071 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3103 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building