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In Section 4, we describe the proposed distributed Gram-Schmidt orthogonalization algorithm with simultaneous refinements of all elements (DS-CGS).
This first solved structure of wagnerite was used as a parent model for structural refinements of all wagnerite crystals.
Refinements of all three structures using REFMAC5 (30) and XFIT (31) led to Rfree values of 0.23, 0.29, and 0.26, respectively.
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The structure was solved by direct methods and the refinement of all non-hydrogen atoms was performed with SHELX97 [33].
Successive steps of manual refinement of all nine subunits using COOT [49] allowed tracing of more flexible regions as well as locating three sulfate ions at catalytic core domains., Multiple rounds of manual fitting followed by restrained and rigid body refinement in Refmac5 [48] reduced Rwork/Rfree to 0.31/0.34 and positioned all three Rrp4 proteins into density map.
Similar protocols were applied in the refinement of all structures.
Anisotropic B factors were used during the refinement of all D139 mutant structures.
Full-matrix least-squares refinement of all data sets was carried out using JANA2006 (Petříček et al., 2006 ▶).
Details of the data collection, processing, and refinement of all three structures are summarized in Table 1.
We estimate that the parallel stochastic refinement is on average about 20 to 40 fold faster in comparison to the independent refinement of all candidate orientations.
All C H hydrogen positions were calculated in the idealized positions by using a riding atom model after the anisotropic refinement of all non-hydrogen atoms of the structure.
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