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B-DNA with 7-deaza-dG modification
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 Droplets containing 0.6 mM oligonucleotide, 5% 2-methyl-2,4-pentanediol (MPD), 20 mM sodium cacodylate (pH 6.0), 6 mM spermine tetrahydrochloride, 40 mM KCl and 10 mM MgCl2 were equilibrated against a reservoir of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.185 α = 90 b = 40.328 β = 90 c = 65.686 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 34.36 96.4 0.049 6.2 9994 8678
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 86.7 0.118 4.6 153
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 34.36 2 2 9994 7824 831 96.59 0.18855 0.18855 0.18205 0.25957 0.2749 RANDOM 22.428
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] 0.48 -0.77 0.29
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.04 r_scbond_it 3.217 r_angle_refined_deg 1.618 r_angle_other_deg 1.144 r_nbd_refined 0.402 r_nbd_other 0.249 r_nbtor_refined 0.244 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_other 0.148 r_nbtor_other 0.083
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.04 r_scbond_it 3.217 r_angle_refined_deg 1.618 r_angle_other_deg 1.144 r_nbd_refined 0.402 r_nbd_other 0.249 r_nbtor_refined 0.244 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_other 0.148 r_nbtor_other 0.083 r_symmetry_hbond_refined 0.077 r_chiral_restr 0.056 r_symmetry_vdw_refined 0.048 r_gen_planes_refined 0.023 r_bond_refined_d 0.006 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_xyhbond_nbd_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 486 Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing