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L-type DNA containing 2'-fluoro-2'-deoxycytidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 291 0.01 M Magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 5.6, 1.8 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.84 α = 90 b = 43.84 β = 90 c = 41.25 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 99 CCD MAR CCD 130 mm 2021-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.987 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.35 21.92 99.2 0.083 0.085 0.018 20.4 19.8 9914
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 97.5 1.645 0.371 2.2
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 7KW4 1.35 21.93 9441 458 99.19 0.18608 0.18434 0.1896 0.22669 0.2231 RANDOM 22.396
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 r_angle_refined_deg 3.396 r_long_range_B_refined 3.333 r_long_range_B_other 3.28 r_scangle_other 2.504 r_angle_other_deg 2.077 r_scbond_it 1.672 r_scbond_other 1.67 r_chiral_restr 0.146 r_bond_other_d 0.046 r_bond_refined_d 0.033
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.396 r_long_range_B_refined 3.333 r_long_range_B_other 3.28 r_scangle_other 2.504 r_angle_other_deg 2.077 r_scbond_it 1.672 r_scbond_other 1.67 r_chiral_restr 0.146 r_bond_other_d 0.046 r_bond_refined_d 0.033 r_gen_planes_refined 0.023 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 324 Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing