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X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (iii) Hexagonal plates with intense spots and a depression
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model InsightII Z-type DNA tetranucleotide built using InsightII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1mM DNA, 75mM sodium cacodylate trihydrate buffer (pH 7.0), 0.5mM cobalt hexammine chloride, 0.75mM spermine, equilibrated against 50% methyl pentane diol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.61 23.723
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.816 α = 90 b = 17.816 β = 90 c = 43.006 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2009-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.7 15.4 100 0.0766 0.0635 4.3 8.71 426 3 65
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 2.7 2.8 100 0.458 0.42 1 8.27 26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Z-type DNA tetranucleotide built using InsightII 2.72 14.52 394 394 24 100 0.24724 0.24474 0.243 0.27738 0.2517 RANDOM 42.419
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.562 r_scangle_it 2.523 r_scbond_it 1.448 r_symmetry_vdw_refined 0.357 r_nbtor_refined 0.322 r_xyhbond_nbd_refined 0.32 r_nbd_refined 0.278 r_symmetry_hbond_refined 0.236 r_chiral_restr 0.114 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.562 r_scangle_it 2.523 r_scbond_it 1.448 r_symmetry_vdw_refined 0.357 r_nbtor_refined 0.322 r_xyhbond_nbd_refined 0.32 r_nbd_refined 0.278 r_symmetry_hbond_refined 0.236 r_chiral_restr 0.114 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 165 Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling