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2'-F modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.783 α = 90 b = 48.783 β = 90 c = 82.434 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 99 PIXEL DECTRIS PILATUS 6M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
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 1.58 50 100 0.038 0.039 0.009 0.999 81.3 18.5 16165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 100 0.33 0.34 0.081 0.999 10.6 17.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5UEE 1.58 50 14745 721 91.165 0.195 0.1936 0.1982 0.2302 0.228 17.073
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] 0.001 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.619 r_lrange_other 5.445 r_scangle_it 3.88 r_scangle_other 3.879 r_angle_other_deg 3.744 r_angle_refined_deg 3.483 r_scbond_it 2.624 r_scbond_other 2.623 r_chiral_restr_other 1.769 r_symmetry_nbtor_other 0.292
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.619 r_lrange_other 5.445 r_scangle_it 3.88 r_scangle_other 3.879 r_angle_other_deg 3.744 r_angle_refined_deg 3.483 r_scbond_it 2.624 r_scbond_other 2.623 r_chiral_restr_other 1.769 r_symmetry_nbtor_other 0.292 r_symmetry_xyhbond_nbd_refined 0.263 r_xyhbond_nbd_refined 0.254 r_nbtor_refined 0.252 r_symmetry_nbd_other 0.21 r_metal_ion_refined 0.159 r_nbd_other 0.159 r_chiral_restr 0.149 r_nbd_refined 0.109 r_symmetry_nbd_refined 0.096 r_bond_other_d 0.031 r_bond_refined_d 0.03 r_gen_planes_refined 0.023 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 488 Solvent Atoms 123 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing