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Structure of Full Length Topoisomerase I from Thermotoga maritima in monoclinic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GAI PDB ENTRY 2GAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 34 % Jeffamine M-600, 100 mM MES/NaOH, 64 mM Sodium Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.82 56.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.049 α = 90 b = 142.714 β = 90.84 c = 127.638 γ = 90
Symmetry Space Group P 1 21 1
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 1.2815 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 1.95 45 99.6 0.12 8.2 116615 116615
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 1.95 2.05 99.1 0.44 2.7
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 2GAI 1.95 15 116577 110740 5837 99.6 0.197 0.197 0.195 0.2045 0.246 0.2549 RANDOM 9.845
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] 0.74 -0.47 0.22 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_4_deg 19.901 r_dihedral_angle_3_deg 15.918 r_dihedral_angle_1_deg 6 r_scangle_it 4.282 r_scbond_it 2.919 r_angle_refined_deg 1.999 r_mcangle_it 1.569 r_mcbond_it 1.435 r_angle_other_deg 1.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_4_deg 19.901 r_dihedral_angle_3_deg 15.918 r_dihedral_angle_1_deg 6 r_scangle_it 4.282 r_scbond_it 2.919 r_angle_refined_deg 1.999 r_mcangle_it 1.569 r_mcbond_it 1.435 r_angle_other_deg 1.082 r_mcbond_other 0.265 r_symmetry_hbond_refined 0.245 r_symmetry_vdw_other 0.216 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.179 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.133 r_chiral_restr 0.117 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9428 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling AMoRE phasing