Table 1 Cryo-EM data collection, refinement and validation statistics
From: Growth phase-dependent reorganization of cryptophyte photosystem I antennae
| Â | PSI-14CACL-phase (EMDB37642) (PDB 8WM6) | PSI-11CACL-phase (EMDB37654) (PDB 8WMJ) | PSI-14CACS-phase (EMDB37659) (PDB 8WMV) | PSI-11CACS-phase (EMDB37660) (PDB 8WMW) |
|---|---|---|---|---|
Data collection and processing | ||||
 Magnification | 130,000 | 130,000 | 130,000 | 130,000 |
 Voltage (kV) | 300 | 200 | 300 | 300 |
 Electron exposure (e–/Å2) | 60 | 60 | 60 | 60 |
 Defocus range (μm) | 1.2–2.3 | 1.2–2.2 | 1.2–2.2 | 1.2–2.2 |
 Pixel size (Å) | 1.04 | 1 | 1.04 | 1.04 |
 Symmetry imposed | C1 | C1 | C1 | C1 |
 Initial particle images (no.) | 345,634 | 326,979 | 281,821 | 427,894 |
 Final particle images (no.) | 86,231 | 41,093 | 42,423 | 31,215 |
 Map resolution (Å) FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
 Map resolution range (Å) | 2.5-3.7 | 2.6-4.2 | 2.8-4.0 | 3.0–4.2 |
Refinement | ||||
 Initial model used (PDB code) | 6LY5, 5ZGB | PSI-14CACL-phase | PSI-14CACL-phase | PSI-14CACL-phase |
 Model resolution (Å) FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
 Model resolution range (Å) | 2.7 | 3.0 | 2.9 | 3.3 |
 Map sharpening B factor (Å2) | -57 | -76 | -55 | -76 |
Model composition | ||||
 Non-hydrogen atoms | 61,164 | 52,744 | 59,342 | 51,054 |
 Protein residues | 5216 | 4540 | 5017 | 4350 |
 Ligands | 415 | 349 | 407 | 342 |
B factors (Ã…2) | ||||
 Protein | 23.85 | 16.29 | 30.52 | 33.63 |
 Ligand | 27.15 | 20.44 | 38.29 | 41.28 |
R.m.s. deviations | ||||
 Bond lengths (Å) | 0.008 | 0.011 | 0.011 | 0.010 |
 Bond angles (°) | 1.452 | 1.601 | 1.737 | 1.492 |
Validation | ||||
 MolProbity score | 1.85 | 1.82 | 1.69 | 1.73 |
 Clashscore | 7.88 | 9.45 | 6.38 | 7.19 |
 Poor rotamers (%) | 1.93 | 1.88 | 1.48 | 2.21 |
Ramachandran plot | ||||
 Favored (%) | 96.82 | 97.48 | 96.65 | 97.65 |
 Allowed (%) | 3.11 | 2.52 | 3.33 | 2.33 |
 Disallowed (%) | 0.08 | 0.00 | 0.02 | 0.02 |
