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Crystal structure of lurbinectedin bound to 10-mer duplex DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal B-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Sodium malonate, potassium chloride, lithium chloride, spermine
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.224 α = 90 b = 112.224 β = 90 c = 112.224 γ = 90
Symmetry Space Group P 41 3 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 PILATUS3 6M 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
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 2.3 39.7 99.95 0.142 0.146 0.032 0.999 16.05 21.1 11334
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 2.3 2.5 100 3.306 3.39 0.745 0.464 1.08 20.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 39.7 10731 567 99.9 0.202 0.2009 0.2005 0.2168 0.2169 55.652
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 r_dihedral_angle_2_deg 42.749 r_lrange_other 10.608 r_lrange_it 10.007 r_scangle_it 9.554 r_scangle_other 9.548 r_scbond_other 8.373 r_scbond_it 8.351 r_angle_refined_deg 3.73 r_dihedral_angle_other_2_deg 1.463 r_angle_other_deg 0.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.749 r_lrange_other 10.608 r_lrange_it 10.007 r_scangle_it 9.554 r_scangle_other 9.548 r_scbond_other 8.373 r_scbond_it 8.351 r_angle_refined_deg 3.73 r_dihedral_angle_other_2_deg 1.463 r_angle_other_deg 0.645 r_symmetry_nbd_refined 0.541 r_nbtor_refined 0.275 r_nbd_refined 0.273 r_nbd_other 0.264 r_symmetry_nbd_other 0.241 r_symmetry_xyhbond_nbd_refined 0.232 r_metal_ion_refined 0.212 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.107 r_gen_planes_refined 0.026 r_bond_refined_d 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 43 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing