☰ Navigation Tabs
Crystal structure of trabectedin-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MJQ DNA only
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 10 mM Tris pH 7.5, 5 mM MgCl2, and 2 mM spermine hydrochloride in the drop, incubated against 19% v/v 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.237 α = 90 b = 47.032 β = 90 c = 50.331 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 EIGER2 X 9M 2025-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.28 50 98.5 0.061 0.976 46 9 4597 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 92.9 0.915
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.28 34 4264 223 98.68 0.23903 0.23799 0.2438 0.25979 0.2538 RANDOM 66.328
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] -3.43 -2.72 6.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.334 r_long_range_B_other 5.332 r_scangle_other 3.637 r_scbond_it 2.35 r_scbond_other 2.349 r_angle_other_deg 1.655 r_angle_refined_deg 1.011 r_chiral_restr 0.057 r_bond_other_d 0.019 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.334 r_long_range_B_other 5.332 r_scangle_other 3.637 r_scbond_it 2.35 r_scbond_other 2.349 r_angle_other_deg 1.655 r_angle_refined_deg 1.011 r_chiral_restr 0.057 r_bond_other_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.012 r_bond_refined_d 0.005 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 488 Solvent Atoms 3 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing