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L-DNA containing 2'-fluoro modification
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.08 M NaCl, 0.02 M MgCl2, 0.04 M Sodium Cacodylate trihydrate pH 5.5, 35% (v/v) MPD, 0.002 M hexammine cobalt(III) chloride
Crystal Properties Matthews coefficient Solvent content 2.36 64.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.33 α = 90 b = 32.33 β = 90 c = 75.58 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 99 CCD MARMOSAIC 300 mm CCD 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.03 28 97.8 0.141 0.143 0.025 0.995 19.9 29.4 12016 9.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.03 1.05 65.9 1.223 0.562 0.346 1.7 5.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1d79 1.03 22.497 1.36 11951 546 97.49 0.1668 0.1665 0.1671 0.1738 0.1704 RANDOM
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 29.949 f_angle_d 4.65 f_chiral_restr 0.436 f_plane_restr 0.054 f_bond_d 0.051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 161 Solvent Atoms 54 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing