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LNA 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 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.769 α = 90 b = 47.769 β = 90 c = 84.122 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 1.71 50 100 0.052 0.054 0.013 0.994 52.3 18.8 12474
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 1.71 1.74 0.475 0.489 0.115 0.994 6.9 17.5
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 1.714 50 11701 611 93.833 0.206 0.2052 0.2098 0.2202 0.2222 15.717
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] -0.005 -0.003 -0.005 0.018
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.342 r_lrange_other 5.103 r_angle_other_deg 3.9 r_angle_refined_deg 3.048 r_scangle_it 2.842 r_scangle_other 2.841 r_scbond_it 2.187 r_scbond_other 2.185 r_chiral_restr_other 1.779 r_xyhbond_nbd_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.342 r_lrange_other 5.103 r_angle_other_deg 3.9 r_angle_refined_deg 3.048 r_scangle_it 2.842 r_scangle_other 2.841 r_scbond_it 2.187 r_scbond_other 2.185 r_chiral_restr_other 1.779 r_xyhbond_nbd_refined 0.305 r_symmetry_nbtor_other 0.292 r_nbtor_refined 0.245 r_symmetry_nbd_other 0.22 r_symmetry_xyhbond_nbd_refined 0.181 r_nbd_other 0.172 r_nbd_refined 0.168 r_chiral_restr 0.135 r_symmetry_nbd_refined 0.08 r_symmetry_xyhbond_nbd_other 0.041 r_bond_other_d 0.032 r_bond_refined_d 0.027 r_gen_planes_refined 0.019 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 378 Solvent Atoms 115 Heterogen Atoms 328
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing