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Structure of d(CACGCG).d(CGCGTG) with low concentration of PdCl2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model InsightII Fiber model of Z-DNA built using insightII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 50mM Sodium Cacodylate, 0.1mM PdCl2, 1.0mM spermine, 40% (v/v) MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.702381 27.748251
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.785 α = 90 b = 30.941 β = 90 c = 44.789 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 293 IMAGE PLATE MAR scanner 345 mm plate mirrors 2008-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.72 25.5 97.9 0.063 0.0482 5.7 4.27 2822 2809 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.72 1.78 96.2 0.33 0.2904 1.8 4.24 279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Fiber model of Z-DNA built using insightII 1.72 25.46 2682 127 97.4 0.21906 0.21804 0.2164 0.23992 0.2337 RANDOM 15.632
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.262 r_angle_refined_deg 2.039 r_scbond_it 1.894 r_nbtor_refined 0.277 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.175 r_chiral_restr 0.077 r_symmetry_hbond_refined 0.048 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.262 r_angle_refined_deg 2.039 r_scbond_it 1.894 r_nbtor_refined 0.277 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.175 r_chiral_restr 0.077 r_symmetry_hbond_refined 0.048 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 246 Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction