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Crystal structure of the Sulfolobus solfataricus topoisomerase III in complex with DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 0.1 M HEPES (pH 6.6), 2.25 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.48 64.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.731 α = 90 b = 150.731 β = 90 c = 97.032 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS PILATUS 2M 2015-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 99.9 0.065 21.7 7.6 39128 50.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.9 0.882 1.9 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.5 50 37280 1939 99.92 0.22197 0.22008 0.2137 0.259 0.2613 RANDOM 49.085
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] 2.16 2.16 -4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 18.53 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 8.908 r_long_range_B_refined 7.251 r_long_range_B_other 7.218 r_scangle_other 6.689 r_scbond_other 5.105 r_scbond_it 5.104 r_mcangle_it 4.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 18.53 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 8.908 r_long_range_B_refined 7.251 r_long_range_B_other 7.218 r_scangle_other 6.689 r_scbond_other 5.105 r_scbond_it 5.104 r_mcangle_it 4.802 r_mcangle_other 4.801 r_mcbond_it 3.594 r_mcbond_other 3.593 r_angle_other_deg 3.511 r_angle_refined_deg 1.215 r_chiral_restr 0.051 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5378 Nucleic Acid Atoms 163 Solvent Atoms 308 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing