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Crystal structure of double-stranded DNA GAGGCCTC; crystals grown in Zn2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 1 mM ds DNA with 5 mM zinc acetate incubated against 55% (v/v) 2-methyl-2,4-pentanediol (MPD)
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.174 α = 90 b = 44.174 β = 90 c = 24.281 γ = 90
Symmetry Space Group P 43 21 2
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 2014-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.078 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 1.65 50 97.1 0.052 10.4 10.4 3080
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 1.65 1.71 99 0.235 10.2
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 1.65 30 2909 141 96.86 0.21607 0.21395 0.2273 0.25535 0.2682 RANDOM 40.991
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] -1.78 -1.78 3.56
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 71.39 r_sphericity_bonded 36.186 r_long_range_B_other 5.559 r_long_range_B_refined 5.546 r_scangle_other 4.402 r_scbond_other 4.322 r_scbond_it 4.307 r_rigid_bond_restr 2.263 r_angle_other_deg 1.382 r_angle_refined_deg 0.817
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 71.39 r_sphericity_bonded 36.186 r_long_range_B_other 5.559 r_long_range_B_refined 5.546 r_scangle_other 4.402 r_scbond_other 4.322 r_scbond_it 4.307 r_rigid_bond_restr 2.263 r_angle_other_deg 1.382 r_angle_refined_deg 0.817 r_chiral_restr 0.06 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 161 Solvent Atoms 12 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing