Primary Citation PubMed: 12112683
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Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.
(2011) BMC Plant Biol 11
PubMed: 21324123 | PubMedCentral: PMC3048497 | DOI: 10.1186/1471-2229-11-33
By contrast, although the REDDD amino acids are conserved in most sTLPs, AM-3D of several sTLP sequences with the recently solved structure of wheat TLX1 (PDB: 1KWN ) revealed neither an acidic cleft ... or any particular conserved region which could be linked to the reported xylanase inhibitor function (Figuer 6 , [ 12 ]).
Publication Year: 2011
Bulk-solvent and overall scaling revisited: faster calculations, improved results.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 23519671 | PubMedCentral: PMC3606040 | DOI: 10.1107/S0907444913000462
For example, considering k isotropic to be a single-value scalar the pair ( k mask , k isotropic ) that minimizes the R factor in the low-resolution range of PDB data set 1kwn is (0.2913, 0.0961), whi... e the pair (0.3218, 0.0863) minimizes the LS function.
Figure 5 Plots of R factors (with k isotropic = 0.0961) and the LS function (with k isotropic = 0.0863) for PDB entry 1kwn (left) and R factors (with k isotropic = 0.0131) and the LS function (with k isotropic = 0.0151) for PDB entry 1hqw (right), illustrating that the minima of the R -factor function (46) and the LS function (22) can be at significantly different locations in parameter space.
Table 1 Comparison of binning schemes performed with d −3 and ln( d ) spacing for three selected PDB data sets: 1kwn , 3hay and 3gk8 All three data sets have very low completeness in the lowest resolution bin, which d −3 binning obscures while ln( d ) binning makes clear even when using approximately half the number of bins.
Table 1 ▶ compares binning performed uniformly in d −3 and in ln( d ) spacing for three data sets (PDB entries 3hay , 1kwn and 3gk8 ).
1kwn 3hay 3gk8 Bin No.
Publication Year: 2013
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