Table 1 Cryo-EM data collection, refinement and validation statistics
#1 DosPFLAG + c-di-GMP (composite) (EMDB-45746) (PDB 9CMF) | #1 DosPFLAG + c-di-GMP (C-Terminal) (EMDB- 45645) | #1 DosPFLAG + c-di-GMP (N-Terminal) (EMDB-45646) | #1 DosPFLAG + c-di-GMP (Consensus) (EMDB-45665) | #2 DosPR97A straight (EMDB-44524) (PDB 9BGV) | #3 DosPR97A bent (EMDB-44646) (PDB 9BKV) | #4 DosP straight (EMDB-45485) (PDB 9CDR) | #5 DosP bent (EMDB-45489) (PDB 9CE0) | DosPR97A + c-di-GMP (composite) (EMDB-45727) (PDB 9CLO) | DosPR97A + c-di-GMP (C-Terminal) (EMDB-45667) | DosPR97A + c-di-GMP (N-Terminal) (EMDB-45669) | DosPR97A + c-di-GMP (Consensus) (EMDB-45670) | |
Data collection and processing | ||||||||||||
Magnification | 81 kx | 81 kx | 81 kx | 81 kx | 81 kx | 81 kx | 105 kx | 105 kx | 165 kx | 165 kx | 165 kx | 165 kx |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
Defocus range (μm) | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 | -0.6 to -1.6 | -0.6 to -1.6 | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 | -0.8 to -2.0 |
Pixel size (Å) | 0.5305 | 0.5305 | 0.5305 | 0.5305 | 0.5328 | 0.5328 | 0.4133 | 0.4133 | ||||
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 9.8 million | 9.8 million | 9.8 million | 9.8 million | 10.5 million | 10.5 million | 5 million | 5 million | 2.5 million | 2.5 million | 2.5 million | 2.5 million |
Final particle images (no.) | 307,809 | 307,809 | 157,857 | 157,857 | 353,471 | 391, 512 | 191,953 | 154,173 | 186,761 | 186,761 | 186,761 | 186,761 |
Map resolution (Å) FSC threshold | 3.11 FSC = 0.143 | 3.83 FSC = 0.143 | 3.7 FSC = 0.143 | 3.65 FSC = 0.143 | 3.43 FSC = 0.143 | 3.91 FSC = 0.143 | 3.97 FSC = 0.143 | 3.09 FSC = 0.143 | 3.18 FSC = 0.143 | 3.45 FSC = 0.143 | ||
Map resolution range (Å) | 3.11-3.83 | 3.09-3.18 | ||||||||||
Refinement | ||||||||||||
Initial model used (PDB code) | PDB 4HU4 PDB 1S66 Alphafold 2 (Uniprot P76129) | - | - | - | DosPFLAG PDB 1S66 PDB 4HU4 | DosPFLAG PDB 1S66 PDB 4HU4 | DosPR97A PDB 1S66 | DosPR97A PDB 1S66 | DosPFLAG PDB 1S66 PDB 4HU4 | - | - | - |
Model resolution (Å) FSC threshold | 3.6 FSC = 0.5 | - | - | - | 3.9 FSC = 0.5 | 3.8 FSC = 0.5 | 7.2 FSC = 0.5 | 6.9 FSC = 0.5 | 3.1 FSC = 0.5 | - | - | - |
Model resolution range (Å) | ||||||||||||
Map sharpening B factor (Å2) | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer | deepemhancer |
Model composition Non-hydrogen atoms Protein residues Ligands | 12716 1576 HEM: 2 MG: 4 OXY: 2 C2E: 2 | 12590 1574 HEM: 2 | 12562 1571 HEM:2 | 12604 1574 HEM: 2 OXY: 2 | 12551 1568 HEM: 2 OXY: 2 | 12680 1574 HEM: 2 MG: 4 C2E:2 | ||||||
B factors (Å2) Protein Ligand | 85.87 77.88 | 77.65 133.97 | 90.45 119.08 | 106.80 168.94 | 135.91 227.53 | 64.94 62.49 | ||||||
R.m.s. deviations Bond lengths (Å) Bond angles (°) | 0.009 0.801 | 0.005 0.692 | 0.006 0.839 | 0.004 0.983 | 0.005 1.001 | 0.009 1.095 | ||||||
Validation MolProbity score Clashscore Poor rotamers (%) | 1.85 9.44 0.00 | 1.99 11.07 0.00 | 2.16 17.52 0.44 | 1.99 11.14 0.00 | 2.14 16.34 0.15 | 1.91 11.25 0.00 | ||||||
Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 94.91 5.09 0.00 | 93.50 6.50 0.0 | 93.74 6.13 0.13 | 93.44 6.37 0.19 | 93.60 6.27 0.13 | 95.03 4.90 0.06 | ||||||
