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X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (ii) Hexagonal plates with spots
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model InsightII Z-type DNA Dinucleotide step 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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.489 α = 90 b = 17.489 β = 90 c = 41.729 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 CCD MAR CCD 165 mm The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror. 2009-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.54 ELETTRA 5.2R
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 3 20 100 0.111 0.0947 3.3 6.8 147 147 3 57.5
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 3.01 3.12 100 0.404 0.352 1 6.67 12
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 Dinucleotide step built using InsightII 3.01 15.15 145 135 10 98.64 0.19924 0.19618 0.1835 0.23283 0.2104 RANDOM 23.785
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] -0.06 -0.03 -0.06 0.09
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.939 r_scangle_it 3.726 r_scbond_it 2.307 r_chiral_restr 0.181 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 81 Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling