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TNA 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, SITTING DROP 7.5 293 0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.165 α = 90 b = 45.165 β = 90 c = 82.831 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 EIGER X 16M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
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 2.2 82.83 99.68 0.103 0.111 0.04 0.996 20 8.9 5325 57.59
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 2.2 2.24 100 0.295 0.312 0.101 0.955 1.3
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 2.2 82.83 5324 290 99.663 0.228 0.225 0.2251 0.2747 0.2769 55.478
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] -0.556 -0.556 1.112
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.328 r_lrange_other 8.324 r_scangle_it 6.744 r_scangle_other 6.742 r_scbond_it 5.028 r_scbond_other 5.025 r_angle_other_deg 4.041 r_angle_refined_deg 2.663 r_chiral_restr_other 1.885 r_symmetry_xyhbond_nbd_refined 0.374
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.328 r_lrange_other 8.324 r_scangle_it 6.744 r_scangle_other 6.742 r_scbond_it 5.028 r_scbond_other 5.025 r_angle_other_deg 4.041 r_angle_refined_deg 2.663 r_chiral_restr_other 1.885 r_symmetry_xyhbond_nbd_refined 0.374 r_nbtor_refined 0.249 r_symmetry_nbd_other 0.229 r_symmetry_nbtor_other 0.228 r_nbd_other 0.211 r_chiral_restr 0.194 r_symmetry_nbd_refined 0.178 r_nbd_refined 0.133 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_other 0.028 r_bond_other_d 0.025 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 378 Solvent Atoms Heterogen Atoms 318
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing