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Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for another 30 minutes, third collection at room temperature
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, KCl, NaCl and spermine tetrachloride
Crystal Properties Matthews coefficient Solvent content 1.68 26.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.355 α = 90 b = 30.778 β = 90 c = 43.104 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 295 PIXEL RIGAKU HyPix-6000HE 2022-02-22 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) 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 2.1 17.65 99.5 0.999 10.7 2 1612 15.94
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 2.1 2.25 0.982
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 2.1 17.65 1.36 1586 142 98.58 0.1492 0.1467 0.1563 0.188 0.1829 12.34
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 29.7255 f_angle_d 0.6671 f_chiral_restr 0.0403 f_bond_d 0.0041 f_plane_restr 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 31 Heterogen Atoms 15
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing PHENIX refinement Coot model building