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Crystal Structure of Tricyclo-DNA: An Unusual Compensatory Change of Two Adjacent Backbone Torsion Angles
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EHV PDB ENTRY 1EHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.75 mM of oligonucleotide, 20 mM sodium cacodylate, 6 mM NaCl, 40 mM KCl and 5% MPD against 0.7 mL of 35% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.587 α = 90 b = 26.587 β = 90 c = 98.238 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 120 CCD ADSC QUANTUM 315 Flat focusing mirror 2007-05-02 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A 2 SYNCHROTRON APS BEAMLINE 5ID-B 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 1.75 32.74 88 0.049 23.2 3.6 7823 6884
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.796 60
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 PDB ENTRY 1EHV 1.75 32.74 6551 332 88.01 0.17829 0.17602 0.1903 0.22495 0.2487 RANDOM 23.477
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] 0.33 0.17 0.33 -0.5
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.576 r_angle_other_deg 1.849 r_scbond_it 1.839 r_angle_refined_deg 1.757 r_nbtor_refined 0.238 r_symmetry_vdw_other 0.233 r_nbd_other 0.197 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.106 r_symmetry_hbond_refined 0.096
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.576 r_angle_other_deg 1.849 r_scbond_it 1.839 r_angle_refined_deg 1.757 r_nbtor_refined 0.238 r_symmetry_vdw_other 0.233 r_nbd_other 0.197 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.106 r_symmetry_hbond_refined 0.096 r_nbd_refined 0.091 r_nbtor_other 0.083 r_metal_ion_refined 0.073 r_chiral_restr 0.068 r_symmetry_metal_ion_refined 0.057 r_gen_planes_refined 0.011 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 93 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing CNS refinement