Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis

Table 1 Summary of crystal parameters, data collection and refinement statistics for PDB 3k9t

	λ₁MAD-Se	λ₂MAD-Se	λ₃MAD-Se
Data collection
Space group	H32
Unit cell parameters (Å)	a = 153.78, b = 153.78, c = 168.38
Wavelength (Å)	0.91837	0.97925	0.97911
Resolution range (Å)	29.1-2.37	29.1-2.44	29.1-2.25
Resolution range (Å)	(2.43-2.37)	(2.50-2.44)	(2.31-2.25)
No. of observations	172,585	157,212	403,378
No. of unique reflections	31,178	28,543	36,347
Completeness (%)	99.9 (100.0)	99.9 (100.0)	100.0 (100.0)
Mean I/σ (I)	9.0 (1.5)	9.2 (1.6)	12.7 (1.9)
R_merge on I^† (%)	18.9 (101.7)	18.3 (93.1)	20.9 (132.1)
R_meas on I^‡ (%)	20.9 (112.3)	20.3 (102.9)	21.9 (138.4)
R_p.i.m. on I^‡‡ (%)	8.8 (47.4)	8.6 (43.4)	6.5 (41.2)
Model and refinement statistics
Resolution range (Å)	29.1-2.37
No. of reflections (total)	31,177^§
No. of reflections (test)	1576
Completeness (%)	100.0
Data set used in refinement	λ₁
Cutoff criteria	\|F\| > 0
R_cryst^¶	0.171
R_free^¶	0.212
Stereochemical parameters
Restraints (RMSD observed)
Bond angles (º)	1.61
Bond lengths (Å)	0.015
Average isotropic B value^†† (Å²)	29.5
ESU^‡‡‡ based on R_free (Å)	0.18
Protein residues/ atoms	422 / 3386
Waters / Zn/ Cl/ Imd/ MRD	221 / 1 / 2 / 1 / 4

Values in parentheses are for the highest resolution shell.
^†R_merge = Σ_hklΣ_i|I_i(hkl) - (I(hkl))|/Σ_hkl Σ_i(hkl).
^‡R_meas = Σ_hkl[N/(N-1)]^1/2Σ_i|I_i(hkl) - (I(hkl))|/Σ_hklΣ_iI_i(hkl)[17].
^‡‡R_p.i.m (precision-indicating R_merge) = Σ_hkl[(1/(N-1)] ^½ Σ_i|I_i (hkl) - < I(hkl) > | / Σ_hklΣ_i I_i(hkl) [19, 20].
^§ Typically, the number of unique reflections used in refinement is slightly less than the total number that were integrated and scaled. Reflections are excluded owing to systematic absences, negative intensities and rounding errors in the resolution limits and unit-cell parameters.
^¶R_cryst = Σ_hkl||F_obs| - |F_calc||/Σ_hkl|F_obs|, where F_calc and F_obs are the calculated and observed structure-factor amplitudes, respectively. R_free is the same as R_cryst but for 5.1% of the total reflections chosen at random and omitted from refinement.
^†† This value represents the total B that includes TLS and residual B components.
^‡‡‡ Estimated overall coordinate error [18].

ISSN: 1471-2105