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STRUCTURE OF THE TOPOISOMERASE II POISON BOUND TO DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 366D DDF073
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 285 0.5 MM DNA, 20 MM SODIUM CACODYLATE BUFFER, PH 6.5, 4 MM MAGNESIUM ACETATE, 1 MM COBALT(II) CHLORIDE, 0.33 MM SPERMINE.4HCL, 1 MM 9-AMINO-[N-(2- DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE AND 9% MPD EQUILIBRATED AGAINST 1 ML OF A SOLUTION OF 45% MPD IN WATER, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.161 α = 90 b = 30.161 β = 90 c = 39.692 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS II FOCUSING MIRROR 1997-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.6 30 98.4 0.029 56.8 24.7 2763 2763
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) 1.6 1.66 97 0.142 5 5.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION ISOMORPHOUS REPLACEMENT THROUGHOUT DDF073 1.6 16 2705 2705 225 98.5 0.1958 0.1945 0.1934 0.256 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1 182.5
RMS Deviations Key Refinement Restraint Deviation s_similar_dist 0.038 s_from_restr_planes 0.023 s_angle_d 0.021 s_bond_d 0.01 s_zero_chiral_vol s_non_zero_chiral_vol s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 120 Solvent Atoms 29 Heterogen Atoms 46
Software Software Software Name Purpose SHELXS phasing SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling