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E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo GCAACTGG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Sodium Citrate,
20%(w/V)PEG 4000, 10% (v/v) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.685 α = 90 b = 120.884 β = 99.344 c = 85.609 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2025-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 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 1.85 60.5 99.6 0.097 0.11 0.051 0.996 8.2 4.5 64910 24.7
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 1.85 1.9 98.7 0.917 1.04 0.481 0.454 1.5 4.6
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 1.85 60.44 1.35 64581 3178 97.76 0.1795 0.1778 0.1781 0.2118 0.2123 31.75
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 18.2044 f_angle_d 1.1408 f_chiral_restr 0.0725 f_bond_d 0.0127 f_plane_restr 0.0114
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms 125 Solvent Atoms 355 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing