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Base Pairing and Structure Insights into the 5-Formylcytosine in RNA Duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 197D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 50 mM HEPES Na (pH 7.0), 50 mM MgSO4, 1.6 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.05 40.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.692 α = 90 b = 45.923 β = 100.85 c = 45.406 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2015-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.24 30 100 0.05 35.4 7.2 35304
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 1.24 1.28 100 0.92 2.1 5.7
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 197D 1.24 25.2 33515 1770 99.88 0.13454 0.13351 0.1404 0.15451 0.1614 RANDOM 18.582
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] 0.34 -0.23 -1.02 0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 22.752 r_sphericity_bonded 12.888 r_rigid_bond_restr 5.846 r_scangle_other 5.248 r_long_range_B_refined 4.713 r_long_range_B_other 4.674 r_scbond_other 3.847 r_scbond_it 3.844 r_angle_refined_deg 2.195 r_angle_other_deg 1.94
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 22.752 r_sphericity_bonded 12.888 r_rigid_bond_restr 5.846 r_scangle_other 5.248 r_long_range_B_refined 4.713 r_long_range_B_other 4.674 r_scbond_other 3.847 r_scbond_it 3.844 r_angle_refined_deg 2.195 r_angle_other_deg 1.94 r_chiral_restr 0.101 r_gen_planes_refined 0.033 r_bond_refined_d 0.02 r_gen_planes_other 0.01 r_bond_other_d 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1014 Solvent Atoms 251 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing