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Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and 2'-Fluoroarabino-Thymidine (faT)
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, 6 mM NaCl and 80 mM KCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.733 α = 90 b = 69.18 β = 92.21 c = 32.831 γ = 90
Symmetry Space Group P 1 21 1
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 1.0 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 1.69 30 95.4 0.094 8.1 15695 15695
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 1.69 1.8 95.8 0.347 2.8
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 NDB entry AD0007/PDB entry 1DPL 1.69 30 15695 15695 805 95.7 0.20401 0.20341 0.2077 0.21543 0.2002 RANDOM 35.247
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] 1.83 0.35 -3.9 2.09
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.395 r_scbond_it 8.055 r_angle_refined_deg 2.59 r_angle_other_deg 1.881 r_xyhbond_nbd_refined 0.454 r_nbd_other 0.337 r_symmetry_hbond_refined 0.316 r_symmetry_vdw_other 0.292 r_nbd_refined 0.285 r_nbtor_refined 0.285
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.395 r_scbond_it 8.055 r_angle_refined_deg 2.59 r_angle_other_deg 1.881 r_xyhbond_nbd_refined 0.454 r_nbd_other 0.337 r_symmetry_hbond_refined 0.316 r_symmetry_vdw_other 0.292 r_nbd_refined 0.285 r_nbtor_refined 0.285 r_chiral_restr 0.226 r_symmetry_vdw_refined 0.192 r_nbtor_other 0.123 r_xyhbond_nbd_other 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_metal_ion_refined r_metal_ion_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 819 Solvent Atoms 169 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling EPMR phasing