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Crystal Structure of 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 5 303 0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.09 α = 90 b = 70.09 β = 90 c = 349.63 γ = 90
Symmetry Space Group P 41 21 2
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 2008-04-23 M SINGLE WAVELENGTH 2 1 x-ray 78 CCD RAYONIX MX-225 2008-04-23 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 2.6 29.5 99.9 0.079 0.074 19 8.1 28160 28151 42.1
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) 2.6 2.72 100 0.572 0.522 3.2 6 3331
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 (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 SAD THROUGHOUT 2.6 29.14 28151 26710 1438 99.96 0.24371 0.24371 0.24132 0.2435 0.28883 0.2929 RANDOM 55.918
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] 2.02 2.02 -4.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_4_deg 18.828 r_dihedral_angle_3_deg 17.444 r_dihedral_angle_1_deg 5.538 r_scangle_it 1.464 r_angle_refined_deg 1.203 r_scbond_it 0.968 r_angle_other_deg 0.89 r_mcangle_it 0.58 r_mcbond_it 0.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_4_deg 18.828 r_dihedral_angle_3_deg 17.444 r_dihedral_angle_1_deg 5.538 r_scangle_it 1.464 r_angle_refined_deg 1.203 r_scbond_it 0.968 r_angle_other_deg 0.89 r_mcangle_it 0.58 r_mcbond_it 0.522 r_symmetry_vdw_other 0.263 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.202 r_nbd_other 0.185 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.15 r_mcbond_other 0.086 r_nbtor_other 0.085 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5967 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 15
Software Software Software Name Purpose MD2-microdiffractometer data collection SHARP phasing REFMAC refinement XDS data reduction SCALA data scaling