☰ Navigation Tabs
Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ECL H365R mutant, apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 287 ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.392 α = 90 b = 79.148 β = 90 c = 141.798 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 103 CCD MARRESEARCH 2001-12-07 M SINGLE WAVELENGTH 2 1 103 CCD MARRESEARCH 2002-02-16
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.95 APS 5ID-B 2 SYNCHROTRON APS BEAMLINE 5ID-B 0.95 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 1.9 35 95.5 0.069 0.061 7.7 3.9 53723
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 H365R mutant, apo form 1.9 70.71 52986 2846 97.89 0.22595 0.22346 0.2267 0.27257 0.269 RANDOM 31.266
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] -0.53 1.16 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.637 r_dihedral_angle_1_deg 3.751 r_scangle_it 3.329 r_scbond_it 1.956 r_mcangle_it 1.411 r_angle_refined_deg 1.321 r_mcbond_it 0.751 r_angle_other_deg 0.726 r_xyhbond_nbd_other 0.305 r_nbd_refined 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.637 r_dihedral_angle_1_deg 3.751 r_scangle_it 3.329 r_scbond_it 1.956 r_mcangle_it 1.411 r_angle_refined_deg 1.321 r_mcbond_it 0.751 r_angle_other_deg 0.726 r_xyhbond_nbd_other 0.305 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.275 r_symmetry_hbond_refined 0.275 r_xyhbond_nbd_refined 0.242 r_nbd_other 0.24 r_symmetry_vdw_other 0.235 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4621 Nucleic Acid Atoms 126 Solvent Atoms 553 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALA data scaling CNS refinement MAR345 data collection CCP4 data scaling CNS phasing