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Structure of topoisomerase domain of topoisomerase V protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CSB Topoisomerase domain of topo-61 strcture (2CSB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1M Sodium citrate pH 5.5, 23% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.717 α = 90 b = 119.39 β = 90 c = 63.67 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 78 CCD RAYONIX MX-225 2006-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.97872 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 2.4 79.79 94.2 0.117 0.108 8.2 6.9 16304 16259
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) 2.4 2.53 95.7 0.689 0.637 2.2 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT Topoisomerase domain of topo-61 strcture (2CSB) 2.4 79.56 15419 821 99.61 0.2025 0.20004 0.1961 0.24772 0.2424 RANDOM 68.261
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] 3.74 -2.25 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_4_deg 19.025 r_dihedral_angle_3_deg 17.634 r_dihedral_angle_1_deg 5.466 r_scangle_it 5.461 r_scbond_it 3.597 r_mcangle_it 3.044 r_mcbond_it 1.815 r_angle_refined_deg 1.419 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_4_deg 19.025 r_dihedral_angle_3_deg 17.634 r_dihedral_angle_1_deg 5.466 r_scangle_it 5.461 r_scbond_it 3.597 r_mcangle_it 3.044 r_mcbond_it 1.815 r_angle_refined_deg 1.419 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.24 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2203 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction SCALA data scaling AMoRE phasing