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2'-OMe 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 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.972 α = 90 b = 48.972 β = 90 c = 82.204 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 1.44 50 99.9 0.085 0.087 0.02 0.988 26.1 18.7 21287
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 1.44 1.46 99.9 0.497 0.512 0.122 0.985 5.1 15.8
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 1.44 50 18611 889 87.413 0.2 0.1986 0.2024 0.2182 0.2218 15.913
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 0.001 -0.005
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.568 r_lrange_other 4.209 r_angle_other_deg 3.62 r_angle_refined_deg 3.208 r_scangle_it 3.038 r_scangle_other 3.038 r_scbond_it 2.182 r_scbond_other 2.181 r_chiral_restr_other 1.723 r_symmetry_xyhbond_nbd_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.568 r_lrange_other 4.209 r_angle_other_deg 3.62 r_angle_refined_deg 3.208 r_scangle_it 3.038 r_scangle_other 3.038 r_scbond_it 2.182 r_scbond_other 2.181 r_chiral_restr_other 1.723 r_symmetry_xyhbond_nbd_refined 0.303 r_symmetry_nbtor_other 0.286 r_nbtor_refined 0.247 r_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.206 r_nbd_other 0.171 r_chiral_restr 0.138 r_symmetry_nbd_refined 0.119 r_nbd_refined 0.087 r_bond_other_d 0.031 r_bond_refined_d 0.028 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 378 Solvent Atoms 148 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing