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Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 1 mM ds DNA containing 5 mM zinc acetate, 2 mM spermine and 50 mM NaCl,
incubated against 55% (v/v) 2-methyl-2,4-pentanediol (MPD)
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.567 α = 90 b = 42.451 β = 90 c = 49.212 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 MARMOSAIC 300 mm CCD 2014-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.25 50 97.3 0.06 54 6.8 14675
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 1.25 1.27 94.1 0.62 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.26 30 13820 791 96.99 0.21649 0.2143 0.2162 0.25374 0.2559 RANDOM 25.919
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] 4.5 -2.23 -2.27
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.989 r_sphericity_bonded 16.842 r_long_range_B_refined 4.27 r_long_range_B_other 4.186 r_scangle_other 2.17 r_rigid_bond_restr 2.084 r_angle_other_deg 1.955 r_scbond_other 1.861 r_scbond_it 1.86 r_angle_refined_deg 1.146
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.989 r_sphericity_bonded 16.842 r_long_range_B_refined 4.27 r_long_range_B_other 4.186 r_scangle_other 2.17 r_rigid_bond_restr 2.084 r_angle_other_deg 1.955 r_scbond_other 1.861 r_scbond_it 1.86 r_angle_refined_deg 1.146 r_chiral_restr 0.071 r_gen_planes_refined 0.017 r_gen_planes_other 0.012 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 96 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing