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Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form
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 VAPOR DIFFUSION, HANGING DROP 4.8 291 33% Jeffamine M-600, 100 mM sodium citrate/HCl, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.118 α = 83.4 b = 95.421 β = 86.15 c = 96.508 γ = 84.87
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 mirrors 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9756 ESRF ID29
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 1.7 41.56 95.6 0.07 10.5 167812 167812
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 1.7 1.79 95.1 0.44 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ECL 1.7 41.56 167804 159417 8387 95.91 0.199 0.199 0.197 0.2018 0.232 0.2357 RANDOM 12.716
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] 0.78 0.51 0.03 -0.33 0.69 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.575 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 5.263 r_scangle_it 4.644 r_scbond_it 2.86 r_angle_refined_deg 1.758 r_mcangle_it 1.659 r_mcbond_it 1.056 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.575 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 5.263 r_scangle_it 4.644 r_scbond_it 2.86 r_angle_refined_deg 1.758 r_mcangle_it 1.659 r_mcbond_it 1.056 r_nbtor_refined 0.306 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.12 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9428 Nucleic Acid Atoms Solvent Atoms 1054 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling AMoRE phasing