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CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVG PDB entry 1PVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6.5 293 PEG 1500, POTASSIUM CHLORIDE, GLYCEROL, SODIUM CACODYLATE, pH 6.5, microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.553 α = 90 b = 71.444 β = 90 c = 215.724 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1271 ALS 8.3.1
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 1.9 50 90.8 0.057 0.057 16.1 3.3 65576 60064 28.34
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 1.9 1.97 59.8 0.298 0.298 3.2 2.1
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 1PVG 1.9 45.18 65576 60064 5512 90.79 0.19911 0.19911 0.19565 0.1945 0.23741 0.2352 RANDOM 27.203
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] 2.22 -0.98 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.803 r_scangle_it 3.248 r_scbond_it 1.956 r_mcangle_it 1.187 r_angle_refined_deg 1.038 r_mcbond_it 0.609 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.803 r_scangle_it 3.248 r_scbond_it 1.956 r_mcangle_it 1.187 r_angle_refined_deg 1.038 r_mcbond_it 0.609 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6110 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing