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Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 from cocktail soak
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.111 α = 90 b = 105.642 β = 90 c = 194.95 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 93 CCD MARMOSAIC 300 mm CCD 2016-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.81 50 97.8 0.071 0.036 29.2 4.2 93819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.84 98.5 0.882 0.501 0.622 2.3 3.8
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 FREE R-VALUE 1.81 40.988 1.34 93775 2000 97.7 0.1872 0.1863 0.1867 0.2267 0.2269
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 5.525 f_angle_d 0.836 f_chiral_restr 0.057 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7007 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing