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X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 120 mM Magnesium Acetate, 50 mM Sodium Cacodylate pH 6.5, 28% w/v PEG-4000, 1 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.32 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.303 α = 80.06 b = 35.425 β = 84.09 c = 45.128 γ = 81.77
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Rh coated flat mirror, toroidal focusing mirror 2009-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 50 96 0.092 15.6 2.9 17639 17639
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.77 1.83 85.2 0.389 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1AIO 1.77 44.31 17624 16745 891 96.25 0.17342 0.17212 0.1747 0.19788 0.199 RANDOM 39.042
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] -0.53 0.09 1.75 -0.34 1.31 0.03
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.84 r_scbond_it 1.895 r_angle_refined_deg 1.883 r_mcbond_it 0.315 r_nbd_other 0.265 r_nbtor_refined 0.263 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_other 0.166 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_refined 0.146
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.84 r_scbond_it 1.895 r_angle_refined_deg 1.883 r_mcbond_it 0.315 r_nbd_other 0.265 r_nbtor_refined 0.263 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_other 0.166 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_refined 0.146 r_nbd_refined 0.105 r_chiral_restr 0.08 r_nbtor_other 0.074 r_metal_ion_refined 0.041 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_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 972 Solvent Atoms 148 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling