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Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 MOPS, spermine, barium chloride, MPD
Crystal Properties Matthews coefficient Solvent content 2.02 39.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.055 α = 90 b = 54.44 β = 90 c = 21.419 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2023-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.2 27.62 99.3 0.078 0.08199999999999999 0.9990000000000001 22.73 12.3 12268
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 1.2 1.23 0.32299999999999995 0.336 0.992
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7D31 1.2 27.62 1.44 12263 1228 99.14 0.1814 0.1787 0.1809 0.2049 0.2049
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 33.308 f_angle_d 1.346 f_plane_restr 0.051 f_chiral_restr 0.044 f_bond_d 0.019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 305 Solvent Atoms 67 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing