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Sequence and structure of a self-assembled 3-D DNA crystal: D(GGATACGTAGGAG)
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 120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.04 59.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.805 α = 90 b = 40.805 β = 90 c = 51.668 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 2.27 35.34 0.037 16.4 2.8 2219
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 2.27 2.4 1.273 1 2.9 321
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 2.27 35.34 2003 197 96.36 0.20616 0.20244 0.2025 0.24394 0.2421 RANDOM 97.348
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] 0.19 0.09 0.19 -0.61
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.712 r_long_range_B_other 5.697 r_scangle_other 4.511 r_scbond_it 2.73 r_scbond_other 2.704 r_angle_other_deg 1.682 r_angle_refined_deg 1.294 r_chiral_restr 0.078 r_gen_planes_refined 0.01 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.712 r_long_range_B_other 5.697 r_scangle_other 4.511 r_scbond_it 2.73 r_scbond_other 2.704 r_angle_other_deg 1.682 r_angle_refined_deg 1.294 r_chiral_restr 0.078 r_gen_planes_refined 0.01 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 1 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement