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Crystal structure of an N-terminal 44 kDA fragment of topoisomerase V in the presence of dioxane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CSB N-terminal 31 kDa topoisomerase domain of Topo-61 (2CSB) structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 303 0.1M phospate citrate pH 5, 0.2 M NaCl, 15% PEG 3350, 8% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.15 α = 90 b = 47.74 β = 112.48 c = 81.223 γ = 90
Symmetry Space Group C 1 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 78 CCD RAYONIX MX-225 2005-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.96500 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.815 75.05 98.3 0.046 0.04 23 4.1 33609 32998 18.832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.815 1.91 88.6 0.194 0.163 6.8 3.1 4301
Refinement Statistics Diffraction ID Structure Solution 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 N-terminal 31 kDa topoisomerase domain of Topo-61 (2CSB) structure 1.815 28.056 1.35 31317 1673 98.2 0.1771 0.1748 0.1713 0.22 0.2177 random
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] -4.6395 1.4213 0.8795 3.76
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.074 f_angle_d 0.92 f_chiral_restr 0.065 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3081 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing PHENIX refinement XDS data reduction SCALA data scaling