The Mg-free complex (IIo) showed the least deviation from the starting structure, with an rmsd of 1.15 A, while the values for the Mg <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0009142.e026.PNG" class= inline-graphic"/> -containing structures IIm1 and IIm2 were larger by 0.2 to 0.4 A, respectively, with correspondingly higher standard deviations.
When expressed as the fractional deviation from the starting CD value, extrapolation of the linear regression to k1,cd=0 s−1 yielded an intercept of 0.0807, indicating that one of the components had lost about 8% of the measured secondary structure signal at 222 nm with respect to the monomer.
During the simulation, the total root mean square deviation, RMSD, from the starting coordinates was followed in various regions of the protein, Fig. 1A 1C.
Structural modifications of the hTop1-DNA complex during the 25 ns long simulations, in presence or absence of topotecan, can be monitored by measuring the deviation of each structure from the starting crystallographic coordinates after a superposition on the protein Cα atoms.
A total of 3,130 women and 1,576 men using TNF antagonists with an overall age of 50 ± 15 years (mean ± standard deviation) were registered in BIOBADASER from the starting date in February 2000 until September 2004.
The proteins have been analyzed in the last 10 ns of the trajectory (i.e. from 5 ns to 15 ns), where the three systems reach a conformational stability, as monitored by time evolution of the global Root Mean Square Deviation (RMSD), i.e. the displacement from the starting structure (see Figure S1 of Supplementary Data).
Positional root mean square deviations (RMSD) were calculated on the Cα atoms from the starting configuration of the solvated system.
She said: "I would expect Matt's lawyers to argue that there should be a deviation from the normal starting point of equality of assets.
Internal rotation and external rotation were measured as the deviation from the zero starting position, in which the longitudinal axis of the leg was perpendicular to the transverse line across the anterior superior iliac spines.
The root-mean-square deviation of the final structure was 1.88 Å from the starting model.
