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. Author manuscript; available in PMC: 2021 Jul 4.
Published in final edited form as: Nat Struct Mol Biol. 2021 Jan 4;28(2):162–172. doi: 10.1038/s41594-020-00541-x

Table 1.

Cryo-EM data collection, refinement and validation statistics of wildtype ScSec and wildtype and mutant TlSec complexes

ScSec
[Sec62−]
(EMD-22770,
PDB 7KAH)
ScSec[C1]
(EMD-
22771,
PDB
7KAI)
ScSec[C2]
(EMD-
22772, PDB
7KAJ)
TlSec
[Sec62−]
(EMD-22773,
PDB 7KAK)
TlSec
[Plug-open]
(EMD-22774,
PDB 7KAL)
TlSec
[Plug-closed]
(EMD-22775,
PDB 7KAM)
ΔSec62 TlSec
(EMD-22776,
PDB 7KAN)
Δanchor
TlSec (EMD-
22777)
Data collection and processing
Magnification 64,000x 64,000x 64,000x 36,000x 36,000x 36,000x 36,000x 64,000x
Voltage (kV) 300 300 300 200 200 200 200 300
Electron exposure
(e2) 49.1 49.1 49.1 50.0 50.0 50.0 50.0 49.1
Defocus range (μm) −0.8 to −2.5 −0.8 to −2.5 −0.8 to −2.5 −0.6 to −2.4 −0.6 to −2.4 −0.6 to −2.4 −0.9 to −2.2 −0.7 to −2.9
Pixel size (Å) 1.19 1.19 1.19 1.14 1.14 1.14 1.14 1.19
Symmetry imposed C1 C1 C1 C1 C1 C1 C1 C1
Initial particle
images (no.) 2,686,839 2,686,839 2,686,839 1,632,659 1,632,659 1,632,659 546,712 229,825
Final particle images
(no.) 391,885 193,263 193,661 155,601 114,704 143,227 222,047 76,726
Map resolution (Å) 3.1 3.2 3.1 3.9 4.0 3.8 3.7 4.4
 FSC threshold 0.143 0.143 0.143 0.143 0.143 0.143 0.143 0.143
Map resolution range (Å) 2.6 – 11 2.8 – 12 2.7 – 12 3.4 – 13 3.3 – 13 3.3 – 12 3.3 – 12 3.7 – 14
Refinement
Initial model used PDB 6N3Q PDB 7KAH PDB 7KAH PDB 7KAN PDB 7KAN PDB 7KAN PDB 6N3Q -
Model resolution (Å) 3.2 3.3 3.3 4.1 4.2 4.0 4.0 -
 FSC threshold 0.5 0.5 0.5 0.5 0.5 0.5 0.5 -
Map sharpening B factor (Å2) 86.6 80.8 75.9 110.3 90.7 105.2 127.8 -
Model composition
 Non-hydrogen atoms 10,495 10,718 10,712 10,438 10,794 10,921 10,661 -
 Protein residues 1,349 1,399 1,399 1,371 1,429 1,445 1,371 -
 Ligands - - - - - - 2 -
B factors (Å2)
 Protein 73 61 58 117 126 74 30 -
 Ligand - - - - - - 34 -
R.m.s. deviations
 Bond lengths (Å) 0.003 0.003 0.003 0.002 0.002 0.003 0.003 -
 Bond angles (°) 0.522 0.508 0.513 0.524 0.489 0.521 0.623 -
Validation
MolProbity score 1.43 1.42 1.33 1.51 1.42 1.48 1.55 -
Clashscore 4.61 4.14 3.87 6.33 5.62 5.60 6.18 -
Poor rotamers (%) 0 0 0 0 0 0 0 -
Ramachandran plot          
 Favored (%) 96.83 96.58 97.01 97.09 97.42 96.96 96.72 -
 Allowed (%) 3.17 3.42 2.99 2.91 2.58 3.04 3.28 -
 Disallowed (%) 0 0 0 0 0 0 0 -