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1 Supplementary Figure 1 The distribution of chlorophyll containing complexes eluted from DEAE-cellulose column in a sucrose gradient tube Six pigment-containing bands were resolved and identified as: B1, LHCII monomers; B2, LHCII trimers; B3, PSII core; B4-B6, PSI-LHCI. The main PSI-LHCI containing band B4 was isolated and subsequently used for crystallization. Supplementary Figure 2 Purification of pea PSI Samples from selected purification procedure stages are presented. MW; lane 1: thylakoid membranes; lane 2: thylakoid membranes after removing of ATP-synthase and PSII; lane 3: first dark-green fraction of DEAE-cellulose column; lane 4: fraction loaded on sucrose gradient; lane 5: material used for crystallization. A likely subunit distribution is indicated. Supplementary Figure 3 Typical plant PSI crystals Crystals that were crystallized in ammonium citrate and ph 6.7 conditions (on the left) grew in shape of elongated thin plates. Crystals that were crystallized in succinic acid and ph 6.0 conditions (on the right) grew to smaller sizes with quadrangle shape and wider thickness. The final volume of the crystallization drop was 4 _l (1:1 protein : precipitant) in a 6 mm diameter well. Supplementary Figure 4 Anisotropy analysis of the two crystal forms (a) Anisotropy analysis results of crystals grown in ph 6.7 conditions. (b) Anisotropy analysis of crystals grown in ph 6.0 conditions. The F/sigma (structure factor / average error) is plotted for the three principle directions of the crystal (red, green, blue) against the resolution limit. Values of F/sigma < 3 are generally considered as not recommended for consideration for X-ray crystal structure determination. For the new crystal form (b) the anisotropy is significantly improved along axes a and c, which proposes a better crystal packing. The anisotropic analysis was performed with Diffraction Anisotropy Server [38]. Supplementary Figure 5 Examples of improved electron density at 3.3 Å resolution On the left, electron density (blue, with contour level 1 _) for Chl1132 (a), embedded in PsaA (wheat) and for Chl1226 (c) embedded in PsaB (wheat) at 3.4 Å resolution [16]. The circular orientation of the porphyrin rings could not be determined and the phytol chains could not be traced due to the limited electron density. On the right (b, d), nearly the same view of respective Chl molecules with corresponding electron density at 3.3 Å resolution allows identification of additional structural elements. Supplementary Figure 6 PsaR polypeptide Additional electron density (blue, with contour level 1.2 _) observed between PsaK and Lhca3 subunits, view along the membrane normal. PsaR polypeptide was modeled into the electron density as polyalanine transmembrane helix (lightblue ribbon). The rest of PSI is shown in wheat. Subunits PsaK and Lhca3 are indicated. Chlorophylls of the core complex are green, chlorophylls of the LHCI are blue. Supplementary Figure 7 Interface of the core complex facing LHCI On the left, view from the stroma; on the right, view from lumen. PSI core complex is shown in ribbon and surface representation according to the color scheme used in Figure 3. LHCI is shown in ribbon, Lhca1 in green, Lhca4 in yellow, Lhca2 in cyan and Lhca3 in pink, gap chlorophylls which are located between Lhca2/Lhca4 and the core are in red sticks. Additional chlorophylls and subunit PsaN were removed for clarity.

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9 Supplementary Table 1 Data collection statistics Dataset Native 1 Native 2 Native 3 Ref [16] X-ray source ID23-2, ESRF ID23-2, ESRF PXI, SLS ID23-2, ESRF Wavelength (Å) Resolution (Å) Space group P21 P21 P21 P21 Cell, a x b x c (Å) 121x189x x189x x190x x189x127 Cell, ß (º) Unique reflections Redundancy Completeness 99.0 (95.2) 98.2 (94.0) 97.3 (78.5) 91.2 (78.6) Rmerge (%) 0.10 (0.40) 0.13 (0.37) 0.13 (0.37) 0.14 (0.44) I/σI 17.2 (2.8) 14.1 (3.6) 14.1 (2.3) 16.6 (3.5) * Values for the highest resolution shell are shown in parentheses. Crystallographic refinement statistics Dataset Native 1 Native 2 Native 3 Ref [16] Resolution (Å) R work /R free 36/36 37/37 39/42 35/40 Number of atoms RMSD bond (Å) RMSD angle (º) Average B-factor (Å 2 )