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3'-deoxy 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 6 293 0.02 M Magnesium sulfate hydrate, 0.002 M Cobalt (II) chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine
Crystal Properties Matthews coefficient Solvent content 2.98 58.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.822 α = 90 b = 46.822 β = 90 c = 83.199 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 CCD ADSC QUANTUM 315r 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1 ALS 8.2.2
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 1.65 50 99.8 0.084 0.09 0.03 1 23.1 10 13195
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 1.65 1.68 99.4 0.393 0.418 0.142 0.987 4.5 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 1.652 27.748 11790 553 89.008 0.21 0.2081 0.2119 0.2394 0.2489 15.582
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] -0.002 -0.001 -0.002 0.006
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 4.099 r_lrange_it 3.845 r_lrange_other 3.694 r_angle_refined_deg 2.876 r_scangle_it 2.275 r_scangle_other 2.274 r_scbond_it 1.891 r_scbond_other 1.89 r_chiral_restr_other 1.883 r_chiral_restr 0.461
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 4.099 r_lrange_it 3.845 r_lrange_other 3.694 r_angle_refined_deg 2.876 r_scangle_it 2.275 r_scangle_other 2.274 r_scbond_it 1.891 r_scbond_other 1.89 r_chiral_restr_other 1.883 r_chiral_restr 0.461 r_symmetry_nbtor_other 0.275 r_nbtor_refined 0.251 r_xyhbond_nbd_refined 0.241 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.205 r_nbd_other 0.192 r_nbd_refined 0.086 r_symmetry_nbd_refined 0.082 r_bond_other_d 0.031 r_bond_refined_d 0.025 r_gen_planes_refined 0.016 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 378 Solvent Atoms 123 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing