☰ Navigation Tabs
Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D6M PDB ENTRY 1D6M, 1I7D experimental model PDB 1I7D PDB ENTRY 1D6M, 1I7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.8 67.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.26 α = 90 b = 102.26 β = 90 c = 445.61 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 225 mm CCD 2003-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9479 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 2.5 29.132 96.5 0.06 0.06 8.7 4 79675
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) 2.5 2.56 93 0.328 0.328 2.3 2.5 5552
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 PDB ENTRY 1D6M, 1I7D 2.5 29.132 79661 3992 95.74 0.219 0.217 0.2087 0.26 0.2493 RANDOM 45.063
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] 0.55 0.55 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.846 r_dihedral_angle_4_deg 18.858 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.22 r_scbond_it 1.354 r_angle_refined_deg 1.247 r_mcangle_it 1.019 r_mcbond_it 0.599 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.846 r_dihedral_angle_4_deg 18.858 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 5.635 r_scangle_it 2.22 r_scbond_it 1.354 r_angle_refined_deg 1.247 r_mcangle_it 1.019 r_mcbond_it 0.599 r_nbtor_refined 0.304 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10062 Nucleic Acid Atoms 276 Solvent Atoms 147 Heterogen Atoms 11
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction CCP4 data scaling AMoRE phasing