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Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermococcus kodakarensis (Selenomethionine)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 297 2.5 M (NH4)2SO4 with 0.1 M Tris pH 8.0 mixed 1:1 with Protein at 20 mg/ml in 10 mM Tris pH 7.5, 100 mM NaCl, 10% glycerol and 1 mM DTT. Cryoprotection by addition of 1.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.542 α = 90 b = 99.542 β = 90 c = 159.507 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9794 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.98 43.1 100 0.19 0.195 0.046 0.999 12.6 17.6 61936 38.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.02 100 4.63 4.78 1.18 0.471 1.3 16.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.98 43.1 1.33 61936 6236 99.98 0.2021 0.1985 0.2013 0.2333 0.2353 61.93
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4567 f_angle_d 0.9948 f_chiral_restr 0.0579 f_bond_d 0.0093 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2638 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling CRANK2 phasing