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Racemic crystal structure of a synthetic DNA Hairpin with diquinoline linker.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 200, MES, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.04 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.517 α = 105.616 b = 30.04 β = 105.767 c = 45.224 γ = 94.343
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 EIGER2 X 16M Toroidal mirror 2023-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.5 28.56 0.9 0.03446 0.04873 0.998 13.98 2 3985 49.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 89 0.1918 0.2712 0.901 5.53 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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 28.56 3985 382 90.179 0.283 0.2832 0.2782 0.2762 0.3279 0.328 34.254
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] -2.019 5.863 -2.551 12.265 -4.386 -10.245
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 9.472 r_scangle_it 5.944 r_scbond_it 4.54 r_angle_refined_deg 1.96 r_nbtor_refined 0.334 r_xyhbond_nbd_refined 0.271 r_nbd_refined 0.233 r_symmetry_xyhbond_nbd_refined 0.189 r_symmetry_nbd_refined 0.173 r_metal_ion_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 9.472 r_scangle_it 5.944 r_scbond_it 4.54 r_angle_refined_deg 1.96 r_nbtor_refined 0.334 r_xyhbond_nbd_refined 0.271 r_nbd_refined 0.233 r_symmetry_xyhbond_nbd_refined 0.189 r_symmetry_nbd_refined 0.173 r_metal_ion_refined 0.16 r_chiral_restr 0.085 r_gen_planes_refined 0.014 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 401 Solvent Atoms 175 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing