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Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CSB PDB entry 2CSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 303 50 mM HEPES pH 7, 0.1 M KCl, 0.01 M MgCl2, and 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.634 α = 90 b = 161.634 β = 90 c = 58.227 γ = 120
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 300 mm CCD 2010-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.91 29.1 99.5 0.069 0.076 20.6 6.2 19283 35.4
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) 1 2.91 3.04 96.5 0.566 0.519 3.4 6.3 2264
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 2CSB 2.91 29.1 19283 18292 989 99.55 0.20473 0.20473 0.20141 0.204 0.267 0.267 RANDOM 73.398
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] -2.21 -1.11 -2.21 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 16.226 r_dihedral_angle_1_deg 5.434 r_scangle_it 1.584 r_scbond_it 1.086 r_angle_refined_deg 1.035 r_angle_other_deg 0.817 r_mcangle_it 0.555 r_mcbond_it 0.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 16.226 r_dihedral_angle_1_deg 5.434 r_scangle_it 1.584 r_scbond_it 1.086 r_angle_refined_deg 1.035 r_angle_other_deg 0.817 r_mcangle_it 0.555 r_mcbond_it 0.282 r_chiral_restr 0.056 r_mcbond_other 0.039 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4940 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 19
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling