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Crystal structure of the native Z-DNA duplex d(CGCGCG) before soaking of CuCl2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, pH 6.0, KCl, NaCl and spermine tetrachloride
Crystal Properties Matthews coefficient Solvent content 1.65 25.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.283 α = 90 b = 30.764 β = 90 c = 42.477 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 RIGAKU HyPix-6000HE 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.07 18.28 99.6 0.183 0.199 0.077 0.999 11.4 2 10952 4.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.07 1.09 92.7 0.553 0.606 0.241 0.868 3.4
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.07 17.48 1.39 10894 548 99.45 0.1063 0.1053 0.1062 0.1252 0.1255 8.27
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 29.8572 f_angle_d 1.3964 f_chiral_restr 0.0583 f_plane_restr 0.0211 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 88 Heterogen Atoms 14
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing Coot model building PHENIX refinement