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Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ECL PDB ENTRY 1ECL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 DIALYSIS 8 287 ammonium sulfate, pH 8, DIALYSIS, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.99 α = 90 b = 78.705 β = 90 c = 139.328 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 IMAGE PLATE MARRESEARCH 1999-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1
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 1.67 50 98.4 0.066 0.055 8.2 80202 79717 10737.6 26
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 1ECL 1.67 49.39 75645 3997 100 0.20885 0.20845 0.2107 0.21638 0.2163 RANDOM 23.686
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] -1.32 1.28 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.76 r_scangle_it 2.578 r_dihedral_angle_1_deg 1.984 r_scbond_it 1.466 r_angle_refined_deg 1.05 r_mcangle_it 0.982 r_angle_other_deg 0.671 r_mcbond_it 0.502 r_symmetry_vdw_refined 0.261 r_symmetry_vdw_other 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.76 r_scangle_it 2.578 r_dihedral_angle_1_deg 1.984 r_scbond_it 1.466 r_angle_refined_deg 1.05 r_mcangle_it 0.982 r_angle_other_deg 0.671 r_mcbond_it 0.502 r_symmetry_vdw_refined 0.261 r_symmetry_vdw_other 0.228 r_nbd_other 0.214 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_other 0.104 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 4643 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement SCALA data scaling CNS refinement MAR345 data collection CCP4 data scaling CNS phasing