Sentence examples for molecular replacement models from inspiring English sources
First, because of the central role of conformational change in serpin mechanism, it is advisable to consider a variety of molecular replacement models in different conformations and then to allow for rigid-body motions in the initial refinement steps.
Suitable molecular replacement models existed for all of the protein targets of this study.
Conversely, EM maps can be used as molecular replacement models to phase X-ray structures.
The initial molecular replacement models were manually adjusted in COOT, part of the CCP4 Suite (Winn et al, 2011) and refined with REFMAC5 (Murshudov et al, 1997).
The automated molecular replacement program BALBES calculated a number of molecular replacement models and output a potential solution utilizing 3RR1 (31% identical sequence) as the search model.
Starting molecular replacement models were generated using CHAINSAW (Stein, 2008) and the atomic co-ordinates of the chicken B21 MHC class I molecule (PDBID: 3BEV) with the peptide removed.
The GltTkapo structure (PDB ID 4KY0) was used as a molecular replacement model and for MD simulations.
However, the structural divergence was significant enough to prevent either being used as a suitable molecular replacement model for SpGH38, even when shorter, more conserved, features were used.
The liganded structures were determined by molecular replacement via PHENIX, though in these cases the unliganded LsrF structure was used as the molecular replacement model and reflections for the Rfree set were selected randomly rather than in resolution shells.
A single SpGH38 molecule was then used as a molecular replacement model with the 1.9 Å native dataset in PHASER [60], followed by cycles of maximum-likelihood refinement using REFMAC [61] interspersed with manual corrections of the models using COOT [62].
PKG Iβ cGMP and partial-apo structures were subsequently solved at 2.9 Å and 2.75 Å respectively, using the fully refined structure of the PKG Iβ cAMP complex as a molecular replacement model (Fig. 1 and Table 1).
