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Crystal structure of transplatin/B-DNA adduct obtained upon 7 days of soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 7-14% (v/v) 2-methyl-2,4-pentanediol (MPD), 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.56 α = 90 b = 40.39 β = 90 c = 65.67 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 2023-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 34.404 98.9 0.998 13.2 9.7 13972
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 1.4 1.42 100 0.601 0.9 9.5
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 1.4 34.404 12330 591 88.141 0.218 0.2159 0.2221 0.2567 0.2621 15.483
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] 0.058 -0.149 0.091
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.531 r_lrange_other 5.412 r_scangle_it 3.712 r_scangle_other 3.708 r_angle_refined_deg 3.046 r_scbond_it 2.405 r_scbond_other 1.977 r_angle_other_deg 0.494 r_nbd_refined 0.249 r_nbtor_refined 0.245
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.531 r_lrange_other 5.412 r_scangle_it 3.712 r_scangle_other 3.708 r_angle_refined_deg 3.046 r_scbond_it 2.405 r_scbond_other 1.977 r_angle_other_deg 0.494 r_nbd_refined 0.249 r_nbtor_refined 0.245 r_symmetry_nbd_other 0.214 r_xyhbond_nbd_refined 0.17 r_nbd_other 0.155 r_chiral_restr 0.149 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.096 r_metal_ion_refined 0.095 r_symmetry_nbd_refined 0.049 r_gen_planes_refined 0.03 r_bond_refined_d 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 486 Solvent Atoms 109 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing