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. Author manuscript; available in PMC: 2022 May 19.
Published in final edited form as: Nature. 2019 Jul 17;571(7766):580–583. doi: 10.1038/s41586-019-1391-0

Extended Data Table 2. RMSD of overall structure (blue) and TMD region (orange).

Superposition was performed at backbone level and RMSD was calculated at the Cα level. Nterm elbow and Cterm zipper helices were excluded from the superimposition and RMSD calculation. RMSD values of 0.64 Å and 0.70 Å show that the OFopen and OFoccluded conformations determined from the TmrABATP-Vi and TmrAEQBATP datasets, respectively, are very similar.

Tm rABturnover
IFnarrow
(EMD-4773)
(PDB 6RAF)		 TmrABturnover
IFwide
(EMD-4774)
(PDB 6RAG)		 TmrABturnover
URasym
(EMD-4779)
(PDB 6RAL)		 TmrABturnover
URasym*
(EMD-4780)
(PDB 6RAM)		 TmrAEQBC4F
IFwide
(EMD-4781)
(PDB 6RAN)		 TmrAEQBATP-ADP
OFopen
(EMD-4775)
(PDB 6RAH)		 TmrAEQBATP-ADP
OFoccluded
(EMD-4776)
(PDB 6RAI)		 TmrABATPvi
OFopen
(EMD-4777)
(PDB 6RAJ)		 TmrABATPvi
OFoccluded
(EMD-4778)
(PDB 6RAK)
Data collection and processing
Microscope Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2 Titan Krios G2
Camera GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2 GIF Quantum K2
Magnification 130,000 130,000 130,000 130,000 130,000 130,000 130,000 130,000 130,000
Voltage (kV) 300 300 300 300 300 300 300 300 300
Electron exposure (e−/Å2) 62 62 62 62 62 64 64 64 64
Defocus range (μm) -0.8 to -2.8 -0.8 to -2.8 -0.8 to -2.8 -0.8 to -2.8 -0.8 to -2.8 -0.8 to -2.8 -0.8 to -2.8 -0.5 to -2.5 -0.5 to -2.5
Pixel size (Å) 1.077 1.077 1.077 1.077 1.077 1.077 1.077 1.077 1.077
Symmetry imposed CI CI CI CI CI CI CI CI CI
Initial particle images (no.) 4,043,869 4,043,869 4,043,869 4,043,869 2,126,064 2,355,206 2,355,206 1,304,264 1,304,264
(2,340,747)* (2,340,747)* (2,340,747)* (2,340,747)* (418,392)* (1,420,676)* (1,420,676)* (358,656)* (358,656)*
Final particle images (no.) 133,527 208,674 145,913 97,763 44,733 60,950 94,621 44,051 109,080
Map resolution (Å) 3.8 4.2 3.5 3.8 4.2 2.8 2.9 3.5 3.3
   FSC threshold 0.143 0.143 0.143 0.143 0.143 0.143 0.143 0.143 0.143
Map resolution range (Å) 3.4-6.5 3.6-7.8 3.0-5.0 3.4-6.4 3.8-7.1 2.7-4.0 2.7-4.0 3.2-5.5 2.9-4.0
Refinement
Initial model used (PDB code) 5MKK 5MKK 5MKK/4PL0 5MKK/4PL0 5MKK 5MKK/2ONJ 5MKK/4PL0 5MKK/2ONJ 5MKK/4PL0
Model resolution (Å) 3.8 4.2 3.5 3.8 4.2 2.8 2.9 3.5 3.3
   FSC threshold 0.143 0.143 0.143 0.143 0.143 0.143 0.143 0.143 0.143
Map sharpening B factor (Å2) -110 -100 -100 -106 -100 -46 -54 -100 -95
Model composition
   Non-hydrogen atoms 10174 10188 10127 10186 10173 10161 10191 10198 10180
   Protein residues 1280 1282 1275 1281 1287 1278 1281 1282 1280
   Nucleotides 2 2 2 2 - 2 2 2 2
   Water molecules - - - - - 4 6 - -
B factors (Å2)
   Protein 81.4 112.6 58.8 110.0 107.4 73.9 55.7 72.5 41.9
   Nucleotides 99.2 150.4 56.4 113.3 - 52.4 44.1 56.6 32.6
   Water molecules - - - - - 49.4 43.5 --- ---
R.m.s. deviations
   Bond lengths (Å) 0.0078 0.0096 0.0063 0.0164 0.0167 0.0078 0.0084 0.0079 0.0054
   Bond angles (°) 1.55 1.38 1.15 1.94 2.08 1.53 1.35 1.08 1.02
Validation
   MolProbity score 1.59 1.84 1.77 1.72 1.76 1.58 1.71 1.48 1.48
   Clashscore 6.17 10.72 8.15 10.48 9.74 10.02 9.27 4.94 5.19
   Poor rotamers (%) 0.10 0.67 0.00 0.10 0.09 0.00 0.00 0.19 0.00
Ramachandran plot
   Favored (%) 96.23 95.85 95.35 96.94 96.25 97.72 96.63 96.55 96.78
   Outliers (%) 0.31 0.00 0.08 0.24 0.08 0.16 0.00 0.00 0.00