☰ Navigation Tabs
Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 411D Single strand from the duplex of PDB ID 411D.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 Sodium cacodylate (20
mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v)
, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.199 α = 90 b = 33.199 β = 90 c = 68.508 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r Monochromator Si(111) 2009-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 50 95.2 0.058 18.7 17 4208 4006
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 72.4 0.187 5.8 139
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 Single strand from the duplex of PDB ID 411D. 1.75 29.88 3714 291 95 0.23147 0.22786 0.2292 0.28185 0.2853 RANDOM 35.242
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] 1.35 1.35 -2.71
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.99 r_sphericity_bonded 6.083 r_scangle_it 4.519 r_scbond_it 3.515 r_rigid_bond_restr 3.28 r_angle_refined_deg 3.037 r_chiral_restr 0.12 r_bond_refined_d 0.022 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 201 Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling