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Simulated annealing omit maps were calculated using Phenix, and Pymol was used for structural analyses and the preparation of the structural figures ( http://www.pymol.org; accessed 1 August 2013).
Averages were calculated using three spike-ins.
Modeled scattering intensities were calculated using CRYSOL63.
Read counts were calculated using HTSeq-count.
Relative expression levels were calculated using 2−△△Ct method2−△△Ct
Component scores were calculated using regression models.
For comparisons between only two groups, p values were calculated using paired or unpaired t-tests as described in the figure legends.
Cd31+, Ng2+ and isolectin+ areas were calculated using ImageJ software.
The relative expression levels were calculated using the 2−ΔΔCt method2−ΔΔCt
Colony size and RFI of colonies were calculated using ImageJ.
Pairwise average nucleotide identities were calculated using JSpecies54.
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