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Crystal structure of trabectedin 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 6.35 295 MPD, potassium chloride, lithium chloride, spermine
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.078 α = 90 b = 40.942 β = 90 c = 234.506 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 PILATUS 6M 2024-11-24 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 2.4 25.9 99.19 0.072 0.085 0.043 0.998 7 3.8 10587
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 2.4 2.6 99.53 1.15 1.345 0.691 0.662 3.7
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 2.4 25.9 9980 553 99.528 0.229 0.2263 0.2301 0.2856 0.2873 72.766
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] 6.303 1.184 -7.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.133 r_lrange_it 14.249 r_lrange_other 14.247 r_scangle_it 10.095 r_scangle_other 10.093 r_scbond_it 6.733 r_scbond_other 6.733 r_dihedral_angle_other_2_deg 3.828 r_angle_refined_deg 1.972 r_angle_other_deg 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.133 r_lrange_it 14.249 r_lrange_other 14.247 r_scangle_it 10.095 r_scangle_other 10.093 r_scbond_it 6.733 r_scbond_other 6.733 r_dihedral_angle_other_2_deg 3.828 r_angle_refined_deg 1.972 r_angle_other_deg 0.49 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_other 0.265 r_nbtor_refined 0.263 r_symmetry_nbd_other 0.25 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.163 r_metal_ion_refined 0.16 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.09 r_chiral_restr 0.073 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1616 Solvent Atoms 8 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing