Table 1. Overview of cross-links within the nidogen-1 G3/laminin γ1 LEb2–4 complex.

	Cα–Cα distances (Å)
		model	model
cross-linked lysines	1NPE	(best atom-pair constraint score)	(best total score)
K-948 × K-953	10.4	10.9	11.1
K-1128 × K-1165	13.3	12.3	16.0
K-1072 × K-1128	16.7	19.1	16.2
K-948 × K-1144	17.9	16.4	17.6
K-850 (laminin) × K-1072 (nidogen-1)	20.9	17.5	16.9
K-948 × K-1152	22.2	21.2	22.2
K-1032 × K-1072	27.1	27.1	27.0
K-961 × K-1072	28.7	28.0	28.2
K-864 (laminin) × K-1152 (nidogen-1)	32.2	22.4	27.1
K-850 (laminin) × K-953 (nidogen-1)	33.0	29.5	29.4
K-1032 × K-1152	35.8	35.4	35.4
Photo-L-990 × Arg-1038	24.7	23.4	23.5
Photo-L-844 (laminin) × K-1072 (nidogen-1)	33.8	19.4	20.8

Cα–Cα distances of cross-linked residues were determined for the unmodified crystal structure (PDB entry 1NPE) as well as for the Rosetta models with the best Rosetta total score and atom-pair constraint score, respectively (shown in Figure 6). For intermolecular contacts, residues are assigned to the respective protein. All other cross-links are located within nidogen-1.