☰ Navigation Tabs
Sequence and structure of a self-assembled 3-D DNA crystal: D(GGACACGTGGGAG)
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 2.99 58.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.562 α = 90 b = 40.562 β = 90 c = 51.411 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 2.08 29 0.025 23 2.8 2578
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 2.08 2.2 0.395 1.4 1.6 321
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 2.08 20.744 2325 243 88.01 0.21704 0.21678 0.2171 0.21926 0.2425 RANDOM 78.666
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] 0.13 0.06 0.13 -0.42
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 3.917 r_long_range_B_other 3.913 r_angle_other_deg 3.407 r_scangle_other 3.206 r_scbond_other 1.87 r_scbond_it 1.866 r_angle_refined_deg 1.131 r_chiral_restr 0.143 r_gen_planes_refined 0.008 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 3.917 r_long_range_B_other 3.913 r_angle_other_deg 3.407 r_scangle_other 3.206 r_scbond_other 1.87 r_scbond_it 1.866 r_angle_refined_deg 1.131 r_chiral_restr 0.143 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
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