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X-ray structure of 7-deaza-dG and Z3dU modified duplex CGCGAATXCZCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 355D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 Final droplets contain 0.6 mM oligonucleotides, 5% MPD, 20 mM sodium cacodylate, 6 mM spermine tetrahydrochloride, 40 mM KCl and 10 mM MgCl2., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.858 α = 90 b = 41.057 β = 90 c = 66.615 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 100 CCD MAR CCD 165 mm 2007-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 1.6 34.94 93 0.067 8.5 9574 8368
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) 1.6 1.68 62.1 0.133 4.1 821
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 355D 1.6 34.94 2 2 9574 8368 497 93.38 0.18365 0.18112 0.18112 0.23114 0.2508 RANDOM 29.313
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] 1.23 -0.44 -0.79
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.893 r_scbond_it 3.735 r_angle_refined_deg 1.596 r_angle_other_deg 1.096 r_nbd_refined 0.526 r_nbd_other 0.251 r_nbtor_refined 0.249 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_other 0.136
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.893 r_scbond_it 3.735 r_angle_refined_deg 1.596 r_angle_other_deg 1.096 r_nbd_refined 0.526 r_nbd_other 0.251 r_nbtor_refined 0.249 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_other 0.136 r_nbtor_other 0.081 r_chiral_restr 0.064 r_gen_planes_refined 0.024 r_symmetry_vdw_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing