☰ Navigation Tabs
Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPL NDB entry AD0007/PDB entry 1DPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Final droplet composition: 1 mM oligonucleotide, 10% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.277 α = 90 b = 32.469 β = 90 c = 66.749 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 103 CCD MARRESEARCH 2003-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.60914 APS 5ID-B
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 1.19 33.37 93.7 0.063 13.4 21724 21724
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 1.19 1.27 91 0.29 3.7 4020
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 (All) 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 NDB entry AD0007/PDB entry 1DPL 1.19 33.37 21724 21724 2208 93.69 0.15856 0.15856 0.15736 0.1663 0.16922 0.1749 RANDOM 12.888
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] 0.14 0.18 -0.32
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.576 r_scbond_it 2.088 r_angle_refined_deg 1.26 r_angle_other_deg 1.145 r_nbd_refined 0.537 r_nbtor_refined 0.261 r_nbd_other 0.246 r_symmetry_vdw_other 0.224 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.138
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.576 r_scbond_it 2.088 r_angle_refined_deg 1.26 r_angle_other_deg 1.145 r_nbd_refined 0.537 r_nbtor_refined 0.261 r_nbd_other 0.246 r_symmetry_vdw_other 0.224 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.103 r_nbtor_other 0.088 r_chiral_restr 0.062 r_gen_planes_refined 0.015 r_bond_refined_d 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 408 Solvent Atoms 128 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling EPMR phasing