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High resolution 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 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.391 α = 90 b = 48.391 β = 90 c = 82.304 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 2020-07-22 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 1.67 50 100 0.038 0.039 0.009 1 91.25 18.5 13505
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 1.67 1.7 99.8 0.328 0.339 0.083 0.996 7 14.8
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 1.67 50 11862 616 87.925 0.203 0.2017 0.2052 0.2209 0.2247 17.097
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] 0.008 0.004 0.008 -0.026
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.398 r_lrange_other 5.189 r_angle_other_deg 3.845 r_scangle_it 3.675 r_scangle_other 3.674 r_angle_refined_deg 3.072 r_scbond_it 2.397 r_scbond_other 2.395 r_chiral_restr_other 1.83 r_chiral_restr 0.504
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.398 r_lrange_other 5.189 r_angle_other_deg 3.845 r_scangle_it 3.675 r_scangle_other 3.674 r_angle_refined_deg 3.072 r_scbond_it 2.397 r_scbond_other 2.395 r_chiral_restr_other 1.83 r_chiral_restr 0.504 r_symmetry_xyhbond_nbd_refined 0.261 r_nbtor_refined 0.252 r_symmetry_nbtor_other 0.239 r_xyhbond_nbd_refined 0.232 r_symmetry_nbd_other 0.216 r_nbd_other 0.194 r_symmetry_nbd_refined 0.119 r_nbd_refined 0.104 r_bond_refined_d 0.027 r_bond_other_d 0.027 r_gen_planes_refined 0.021 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 511 Solvent Atoms 108 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing