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FANA 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 7 293 2.4 M Sodium malonate pH 7.0, 50 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.82 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.072 α = 90 b = 49.072 β = 90 c = 81.254 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 PILATUS3 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 2.28 50 100 0.113 0.117 0.114 0.999 29.2 18.8 5536
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 2.28 2.32 100 0.491 0.504 0.027 0.972 7.5 19.2
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 2.281 50 5536 298 99.982 0.207 0.2037 0.2056 0.263 0.2725 27.55
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] 0.012 0.006 0.012 -0.039
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.638 r_lrange_other 4.529 r_angle_other_deg 3.786 r_angle_refined_deg 3.366 r_scangle_it 3.247 r_scangle_other 3.246 r_scbond_it 2.296 r_scbond_other 2.294 r_chiral_restr_other 1.733 r_chiral_restr 0.52
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.638 r_lrange_other 4.529 r_angle_other_deg 3.786 r_angle_refined_deg 3.366 r_scangle_it 3.247 r_scangle_other 3.246 r_scbond_it 2.296 r_scbond_other 2.294 r_chiral_restr_other 1.733 r_chiral_restr 0.52 r_symmetry_nbtor_other 0.277 r_symmetry_xyhbond_nbd_refined 0.262 r_nbtor_refined 0.246 r_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.221 r_nbd_other 0.177 r_symmetry_nbd_refined 0.144 r_nbd_refined 0.112 r_symmetry_xyhbond_nbd_other 0.038 r_bond_other_d 0.028 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 378 Solvent Atoms 47 Heterogen Atoms 327
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing