☰ Navigation Tabs
Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl] Thymidine (T*)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 410D pdb entry 410D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.99 38.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.84 α = 90 b = 44.64 β = 90 c = 45.18 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 110 IMAGE PLATE RIGAKU RAXIS IIC Mirrors 1999-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.65 20 95.4 0.102 17.4 6.5 6146 6146 -3
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) 1.65 1.71 70.7 0.175 6.1 2.7 442
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 410D 1.65 20 6099 6099 672 94.9 0.1632 0.1569 0.1906 0.1851 Random 19
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] -0.559 1.014 -0.456
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_improper_angle_d 1.53 c_angle_deg 1.2 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 418 Solvent Atoms 131 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement