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Crystal structure of Topoisomerase V (61 kDa fragment)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 sodium acetate, sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.5 α = 90 b = 86.4 β = 90 c = 175.7 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 100 CCD MARRESEARCH 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.9793 APS 32-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 28.8 99.2 0.095 6.7 3.7 25958 25958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 98.5 0.328 2.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.9 28.8 24588 24591 1319 98.9 0.23973 0.23618 0.2355 0.30787 0.3105 RANDOM 52.119
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] 1.68 0.5 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_3_deg 20.548 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_1_deg 4.826 r_scangle_it 1.2 r_angle_refined_deg 1.111 r_scbond_it 0.657 r_mcangle_it 0.578 r_mcbond_it 0.319 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_3_deg 20.548 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_1_deg 4.826 r_scangle_it 1.2 r_angle_refined_deg 1.111 r_scbond_it 0.657 r_mcangle_it 0.578 r_mcbond_it 0.319 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8390 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction CNS refinement MAR345 data collection XDS data scaling CNS phasing