☰ Navigation Tabs
Structure of M. kandleri topoisomerase V in complex with DNA. 39 base pair symmetric DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DF7 D_1000262487
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 303 Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C.
Crystals started to appear within minutes of setting up the trays in 1:1 or 2:1 well to complex ratio.
Well solution: 2% PEG 8K, 24 mM sodium acetate pH 5.1, 26 mM sodium acetate pH 5.6, 12.5 uM phosphotungstic acid
Crystal Properties Matthews coefficient Solvent content 4.2 70.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.56 α = 90 b = 121.56 β = 90 c = 497.191 γ = 90
Symmetry Space Group P 43 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 CCD RAYONIX MX-300 Monochromator 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 3.17 86.9 82.4 0.079 0.084 1 18.1 8.8 53311 104.42
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 3.17 3.36 25.7 1.33 1.41 0.646 1.5 9.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1000262487 3.17 59.04 1.35 53291 2690 82.38 0.2202 0.2185 0.2164 0.2513 0.2495
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 16.968 f_angle_d 0.441 f_chiral_restr 0.035 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13604 Nucleic Acid Atoms 1617 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing