Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1

Table 1 Summary of crystallographic data and refinement statistics

Crystal	Ferredoxin (2I7F)	Oxygenase (native) (2GBW)	Oxygenase (biphenyl bound) (2GBX)
Space group	P6₅22	P3₁21	P3₁21
Cell parameters
a = b (Å)	62.064	134.96	134.43
c (Å)	238.436	219.89	220.53
Resolution (Å)¹	9.49 – 1.90 Å (1.96 – 1.90 Å)	19.80 -1.70 Å (1.76 -1.70 Å)	43.15 – 2.75 (2.85 – 2.75)
Data collection
X-ray source	NSLS X6A	IMCA-CAT 17-ID	IMCA-CAT 17-ID
Wavelength (Å)	1.03320	1.00000 Å	1.00000 Å
Total observations	108720	1083097	343108
Unique observations	20866	241600	56040
Completeness (%)¹	93.7 % (65.2 %)	95.3 % (98.1 %)	92.6 % (99.7 %)
(I)/σ(I)¹	8.2 (2.9)	8.2 (2.9)	9.6 (3.7)
Multiplicity¹	5.21 (3.46)	4.48 (4.10)	6.12 (7.14)
R_sym^1,2	0.121 (0.417)	0.083 (0.394)	0.104 (0.409)
Crystallographic refinement
R_factor/R_free (%)³	19.1/20.3	18.8/22.9	22.8/26.9
RMSD from ideality
Bond lengths (Å)	0.017 Å	0.017 Å	0.006 Å
Bond angles (deg)	1.925°	1.616°	0.880°

¹ Outer shell values are in parentheses.
² $R_{s y m} = \frac{\sum_{h k l} \sum_{i} | I_{i} (h k l) - I (h k l) |}{\sum_{h k l} \sum_{i} | I_{i} (h k l) |}$ , where I_i(hkl) is the i th measurement of reflection hkl and I(hkl) is the average for that reflection.
³ $R_{f a c t o r} = \frac{\sum_{h k l} | | F_{o b s} | - k | F_{c a l c} | |}{\sum_{h k l} | F_{o b s} |}$ , where F_obs and F_calc are the observed and calculated structure factors, respectively. R_free is the same, but for a test set of reflections not used in refinement.

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