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Structure of TDP1 complexed with compound IB09
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M MOPS/HEPES pH 7.5, 10% (w/v) PEG 8000, 20% (w/v) ethylene glycol, 0.03M sodium fluoride, 0.03 M sodium bromide, 0.03 sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.023 α = 90 b = 104.748 β = 90 c = 193.241 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 100 PIXEL DECTRIS EIGER X 16M 2022-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0000 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.62 50 94.2 0.061 0.027 0.999 24.7 5.2 122336
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 0.67 0.297 0.803 2
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.62 45.14 1.35 122247 6062 94.11 0.1616 0.1601 0.1613 0.1894 0.1907
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 5.855 f_angle_d 1.443 f_chiral_restr 0.102 f_bond_d 0.018 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6969 Nucleic Acid Atoms Solvent Atoms 755 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing