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Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 MOPS (pH 7), spermine, ammonium nitrate, 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.254 α = 90 b = 46.522 β = 90 c = 76.084 γ = 90
Symmetry Space Group I 2 2 2
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 EIGER X 16M 2017-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.91942 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.007 39.69 99.8 0.044 0.048 0.999 19.23 6.226 5619 47.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.06 98.8 0.287 0.312 0.978 5.24 6.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.01 39.69 1.42 5598 557 99.41 0.2506 0.2469 0.2486 0.2819 0.2801 46.4802
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 36.422 f_angle_d 1.387 f_chiral_restr 0.054 f_bond_d 0.013 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction