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Sequence and structure of a self-assembled 3-D DNA crystal: D(GGATAATTAGGAG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P1Y PDB ENTRY 1p1y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 Self-assembling 3D DNA crystal
120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.177 α = 90 b = 40.177 β = 90 c = 53.015 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 100 PIXEL DECTRIS PILATUS 6M-F 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979200 APS 24-ID-C
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 2.19 34.79 0.024 31.2 5.5 2540
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 2.19 2.31 1.369 1.1 5.3 375
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 1p1y 2.19 34.79 2285 217 98.19 0.22308 0.2223 0.2252 0.23105 0.2378 RANDOM 97.421
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 0.24 0.48 -1.55
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.755 r_long_range_B_other 10.743 r_scangle_other 8.173 r_scbond_other 4.699 r_scbond_it 4.685 r_angle_other_deg 1.705 r_angle_refined_deg 1.081 r_chiral_restr 0.077 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.755 r_long_range_B_other 10.743 r_scangle_other 8.173 r_scbond_other 4.699 r_scbond_it 4.685 r_angle_other_deg 1.705 r_angle_refined_deg 1.081 r_chiral_restr 0.077 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 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 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 254 Solvent Atoms 2 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement