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Sequence and structure of a self-assembled 3-D DNA crystal: D(GGATAGCTAGGAG)
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 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.78 α = 90 b = 40.78 β = 90 c = 51.813 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 2.32 35.32 0.03 21.1 2.9 2079
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 2.32 2.45 0.582 1.6 2.9 317
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 2.32 35.32 1878 192 95.39 0.20549 0.20293 0.21 0.23145 0.2419 RANDOM 91.721
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 7.684 r_long_range_B_refined 7.683 r_scangle_other 6.684 r_scbond_it 4.314 r_scbond_other 4.263 r_angle_other_deg 3.517 r_angle_refined_deg 1.161 r_chiral_restr 0.132 r_gen_planes_refined 0.009 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 7.684 r_long_range_B_refined 7.683 r_scangle_other 6.684 r_scbond_it 4.314 r_scbond_other 4.263 r_angle_other_deg 3.517 r_angle_refined_deg 1.161 r_chiral_restr 0.132 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 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 3 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement