Table 1.
Data and refinement statistics
| Space group | P63 | ||
| Unit cell parameters | a = 283.70 Å, b = 283.70 Å, c = 165.29 Å | ||
| Data collection | |||
| Wavelength (Å) | 1.00 | ||
| Resolution range (Å) | 65.2–6.0 | ||
| Number of observations | 110202 | ||
| Number of unique reflections | 18989 | ||
| Completeness (%) | 99.3 (100)a | ||
| Mean I/σ(I) | 3.5 (2.9)a | ||
| Rmerge on I (%)b | 44.7 (51.3)a | ||
| Rmeas on I (%)c | 49.4 (55.9)a | ||
| Highest resolution shell (Å) | 6.32–6.00 | ||
| Model and refinement statistics for DEN refinement, starting with model M1 | |||
| Resolution range (Å) | 49–7.4 | ||
| No. of reflections (total) | 10004 | Cutoff criteria | |F|>0 |
| No. of reflections (test) | 508 | Rcryst | 0.260d |
| Completeness (%) | 99.5 | Rfree | 0.291d |
| Ramachandran (% favored) | 79 | ||
| Ramachandran (% outliers) | 10.7 | ||
| Stereochemical parameters | |||
| Bond angle RMSD (°) | 1.29 | ||
| Bond length RMSD (Å) | 0.008 | ||
| Average protein isotropic B-factor (Å2) | 120.9 | ||
| Protein | 12 chains with a total of 2334 residues | ||
| Chlorophyll | 96 (95 Chlorophyll a, 1 Chlorophyll a’) | ||
| Beta-carotene | 21 | ||
| Phylloquinone | 2 | ||
| 1,2-dipalmitoyl-phosphatidyl-glycerole | 3 | ||
| 1.2-distearoyl-monogalactosyl-diglyceride | 1 | ||
| Ca2+ | 1 | ||
| FeS | 3e | ||
a
Highest resolution shell.
b
Rmerge= ΣhklΣi | Ii(hkl) − <I(hkl)> |/ΣhklΣi Ii(hkl).
c
Rmeas (redundancy-independent Rmerge) = Σhkl[(n/(n-1)] ½ Σj|Ij(hkl) − <I(hkl)>|/ΣhklΣj Ii(hkl) (Diederichs and Karplus, 1997).
d
R=Σ| |Fobs|−|Fcalc| |/Σ |Fobs| where Fcalc and Fobs are the calculated and observed structure factor amplitudes, respectively. Rfree as for R, but for 5% of the total reflections chosen at random and omitted from refinement. Rcryst as for R, but for the remaining 95% of the reflections.
e
Omitted in refined model for validation purposes.