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. 2020 May 1;2:89–103. doi: 10.1016/j.crstbi.2020.04.005

Table 1.

CryoEM data collection, single-particle reconstruction maps, and model statistics.

Data collection information
Data set EcAGPase-FBP complex EcAGPase-AMP complex
Nominal magnification 47755x 47755x
Voltage (kV) 300 300
Electron dose (e–/Å2) 45.6 44.8
Pixel size (Å) 1.047 1.047
Movie number 2975 1681
Defocus average and range (μm) 1.4 (0.2–2.6) 1.7 (0.3–5.0)
Frames 40 40
Single-particle reconstruction information
Map EcAGPase-FBP complex EcAGPase-AMP complex
Final number of particle images in map 297275 94769
Symmetry imposed D2 C2 C1 D2 C2 C1
EMDB code EMD-4754 EMD-10199 EMD-10201 EMD-4761 EMD-10203 EMD-10208
Map resolution (Å)
FSC=0.143 criterion
3.05 3.16 3.24 2.95 3.09 3.26
Map sharpening
B factor (Å2)
−148.1
−139.9
131.2
−116.8
−114.5
−99.9
Model information

Model
EcAGPase-FBP complex
EcAGPase-AMP complex
PDB ID 6R8B 6SHJ 6SHN 6R8U 6SHQ 6SI8
Atoms (Non-H) 26092 25974 25359 26760 26874 26590
Protein residues 1688 1664 1644 1700 1696 1700
Ligands 4 4 2 4 4 4
Bonds (RMSD)
Length (Å) 0.01 0.01 0.016 0.01 0.01 0.01
Angles (°) 1.34 1.01 1.34 1.35 1.38 1.40
Mean B-factor
Protein 153.64 163.46 94.72 134.96 136.07 88.79
Ligand 176.65 191.65 101.34 127.23 126.19 82.53
MolProbity score 2.11 2.02 1.89 2.30 2.04 1.79
Clashscore 7.93 3.54 2.21 7.17 5.36 2.14
Rotamer outliers (%) 3.12 3.58 4.81 3.32 2.28 2.45
Ramachandran plot
Favored (%) 95.71 92.90 94.47 91.43 92.06 91.31
Allowed (%) 4.05 6.98 5.41 8.57 7.94 8.33
CC (volume) 0.77 0.75 0.80 0.80 0.78 0.79
Mean CC for ligands 0.74 0.66 0.74 0.84 0.82 0.84
CC (mask) 0.77 0.75 0.81 0.80 0.79 0.79