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Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F4Q PDB entry 2F4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 283 30% PEG 400 (w/v), 0.1 M sodium acetate (pH 4.5), 0.2 M calcium chloride.
1:1 molar ratio of protein and DNA, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.67 α = 90 b = 53.44 β = 96.33 c = 77.36 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 100 IMAGE PLATE MAR scanner 345 mm plate Franks mirrors 2006-01-01 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm 2006-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418 2 SYNCHROTRON 1.00
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 1.65 76 96.2 0.053 0.048 24.1 4.7 58613 56385
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) 1.65 1.69 89.5 0.325 0.276 4.1 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2F4Q 1.65 19.824 58613 53565 2820 96.16 0.19487 0.19487 0.19344 0.1996 0.22169 0.2262 RANDOM 13.658
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] 0.3 0.01 -0.72 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.368 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_4_deg 11.133 r_dihedral_angle_1_deg 4.818 r_scangle_it 2.479 r_scbond_it 1.743 r_angle_refined_deg 1.29 r_mcangle_it 1.017 r_angle_other_deg 0.947 r_mcbond_it 0.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.368 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_4_deg 11.133 r_dihedral_angle_1_deg 4.818 r_scangle_it 2.479 r_scbond_it 1.743 r_angle_refined_deg 1.29 r_mcangle_it 1.017 r_angle_other_deg 0.947 r_mcbond_it 0.936 r_symmetry_vdw_other 0.242 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.202 r_nbd_other 0.189 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.185 r_mcbond_other 0.154 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.078 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms 486 Solvent Atoms 281 Heterogen Atoms 9
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling