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X-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, cis-{Pt(NH3)2(pyridine)}2+ Bound to Deoxyguanosine in a Dodecamer Duplex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 120 mM Mg(acetate), 50 mM Na cacodylate, 1 mM spermine, 28% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.44 α = 90 b = 66.01 β = 90 c = 56.05 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315 2007-04-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2007-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.072 APS 24-ID-C 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.984 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 1,2 2.17 50 96 0.107 18.1 6.9 4836 4765
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) 2.17 2.25 76 0.556 6.8 367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.16 28.44 2 4836 4614 216 95.41 0.248 0.227 0.225 0.2261 0.254 0.2538 RANDOM 42.444
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] 0.09 0.04 -0.13
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.387 r_mcbond_it 6.168 r_scbond_it 5.863 r_angle_refined_deg 1.435 r_nbtor_refined 0.349 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.387 r_mcbond_it 6.168 r_scbond_it 5.863 r_angle_refined_deg 1.435 r_nbtor_refined 0.349 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.089 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 486 Solvent Atoms 16 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling