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Crystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 303 0.1 M phosphate citrate pH 5.5, 0.15M sodium sulfate, 0.01M MgCl2, 1 M guanidium hydrochloride, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 1.98 37.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.64 α = 90 b = 80.11 β = 90 c = 137.22 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 78 CCD RAYONIX MX-225 beryllium lenses 2008-07-24 M SINGLE WAVELENGTH 2 1 x-ray 78 CCD RAYONIX MX-225 2008-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G 2 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97915 APS 21-ID-D
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 1.4 28.9 98.8 0.048 0.045 27.5 8.5 138158 136662
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) 1.4 1.46 95.5 0.405 0.379 5.3 7.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.4 28.9 136662 129802 6859 98.68 0.16587 0.16491 0.18424 0.1912 RANDOM 11.181
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] 0.52 -0.32 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_1_deg 4.709 r_scangle_it 2.181 r_scbond_it 1.651 r_angle_refined_deg 1.195 r_angle_other_deg 0.901 r_mcangle_it 0.892 r_mcbond_it 0.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.878 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_1_deg 4.709 r_scangle_it 2.181 r_scbond_it 1.651 r_angle_refined_deg 1.195 r_angle_other_deg 0.901 r_mcangle_it 0.892 r_mcbond_it 0.778 r_symmetry_vdw_refined 0.266 r_symmetry_vdw_other 0.242 r_nbd_refined 0.225 r_nbd_other 0.202 r_nbtor_refined 0.177 r_mcbond_other 0.175 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.138 r_nbtor_other 0.082 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6056 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 52
Software Software Software Name Purpose MD2-microdiffractometer data collection SHARP phasing REFMAC refinement XDS data reduction SCALA data scaling