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Crystal Structure of Deinococcus radiodurans topoisomerase IB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 12% PEG 3350 (w/v), 0.1 M MES (pH 6.5), 0.2 M ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.094 α = 90 b = 64.966 β = 91.78 c = 76.622 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 MARRESEARCH Mirrors 2004-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B .9768 APS 5ID-B
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 1.75 27.5 96.4 0.051 0.044 27.5 6.3 36231 36231
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 1.75 1.8 96.4 0.227 0.213 5.7 3.5 2420
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 1.75 27.5 36231 34411 1819 96.45 0.1992 0.1992 0.19749 0.1981 0.23079 0.2018 RANDOM 35.647
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] 0.69 0.03 -0.18 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.704 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_4_deg 10.157 r_dihedral_angle_1_deg 4.68 r_scangle_it 2.274 r_scbond_it 1.51 r_angle_refined_deg 0.999 r_mcangle_it 0.896 r_mcbond_it 0.632 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.704 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_4_deg 10.157 r_dihedral_angle_1_deg 4.68 r_scangle_it 2.274 r_scbond_it 1.51 r_angle_refined_deg 0.999 r_mcangle_it 0.896 r_mcbond_it 0.632 r_nbtor_refined 0.298 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2458 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling SHARP phasing