Table 1.
Cryo-EM refinement parameters and model validation.
FA CHI | FA-CP CHI | FA-CP POST | |
---|---|---|---|
Map refinement | |||
Number of particles | 178 679 | 303 005 | 40 800 |
Map resolution, half-map FSC0.143 [Å] | 2.49 | 2.02 | 2.44 |
Model statistics | |||
Model composition | |||
Total non-hydrogen atoms | 146 593 | 149 701 | 149 413 |
RNA residues | 4585 | 4585 | 4645 |
Protein residues | 6091 | 6091 | 6103 |
Waters | 0 | 3169 | 1619 |
Mg ions | 169 | 169 | 145 |
General | |||
Map-model FSC0.5 [Å] | 2.5 | 2 | 2.4 |
Map-model CCmask | 0.89 | 0.88 | 0.9 |
MolProbity score | 1.25 | 1.26 | 1.26 |
Clash score | 2.89 | 3.46 | 2.82 |
RMSD bond length [Å] | 0.005 | 0.004 | 0.006 |
RMSD bond angles [°] | 0.633 | 0.632 | 0.682 |
Mean B-factor (protein/nucleotide/ligand/water) | 70.7/74.1/51.2/- | 40.9/35.1/19.7/8.4 | 56.9/61.8/40.8/38.9 |
Protein geometry | |||
Rotamer outliers [%] | 1.05 | 0.99 | 1.24 |
Cß deviations > 0.25 Å [%] | 0 | 0 | 0 |
Ramachandran [%] (Fav./Allow./Outl.) | 97.1/2.9/0.02 | 97.3/2.7/0.02 | 97.4/2.6/0.03 |
Rama-Z (whole/helix/sheet/loop) | 0.05/0.88/-0.20/-0.38 | 0.78/1.80/-0.12/-0.04 | 0.76/1.74/-0.17/0.00 |
CaBLAM [%] (Outl./Disf.) | 0.98/5.14 | 0.92/5.31 | 1.00/5.07 |
CA Geometry outliers [%] | 0.46 | 0.49 | 0.51 |
EMRinger score | 4.21 | 5.48 | 4.32 |
Nucleic acid geometry | |||
Backbone bond length outliers [%] | 0 | 0 | 0 |
Backbone bond angle outliers [%] | 0 | 0 | 0 |
Sugar puckers outliers [%] | 0.48 | 0.50 | 0.43 |
Backbone bond torsion suite outliers [%] | 11.9 | 11.9 | 12.8 |