☰ Navigation Tabs
DNA 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 6.5 293 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 3.05 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.443 α = 90 b = 47.443 β = 90 c = 82.803 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 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
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 1.64 50 99 0.075 0.079 0.026 0.985 24.9 9.6 13719
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 1.64 1.67 97.4 0.314 0.339 0.123 0.989 5.3 5.4
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 1.64 50 12116 569 87.581 0.21 0.2079 0.2114 0.247 0.2592 18.93
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 -0.004
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.73 r_lrange_other 4.501 r_angle_other_deg 3.84 r_scangle_it 2.94 r_scangle_other 2.939 r_angle_refined_deg 2.88 r_scbond_it 2.091 r_scbond_other 2.09 r_chiral_restr_other 1.816 r_chiral_restr 0.481
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.73 r_lrange_other 4.501 r_angle_other_deg 3.84 r_scangle_it 2.94 r_scangle_other 2.939 r_angle_refined_deg 2.88 r_scbond_it 2.091 r_scbond_other 2.09 r_chiral_restr_other 1.816 r_chiral_restr 0.481 r_nbtor_refined 0.252 r_symmetry_nbtor_other 0.244 r_symmetry_nbd_other 0.222 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.129 r_metal_ion_refined 0.105 r_symmetry_xyhbond_nbd_other 0.095 r_nbd_refined 0.09 r_bond_other_d 0.028 r_bond_refined_d 0.023 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 509 Solvent Atoms 112 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing