Skip to main content
. 2005 Jan 12;102(3):646–650. doi: 10.1073/pnas.0409008102

Table 1. Input for the structure calculation and characterization of the energy-minimized NMR structures of ePrP(121–231), mPrP(121–231), and two variants of mPrP(121–231).

Quantity* ePrP mPrP[S170N,N174T] mPrP[N174T] mPrP
NOE upper distance limits 2,254 2,183 2,027 2,264
Dihedral angle constraints 110 110 110 110
Residual target function value, Å2 1.77 ± 0.41 1.67 ± 0.22 1.68 ± 0.32 1.93 ± 0.20
Residual distance constraint violations
   No. >0.1 Å 29 ± 4 35 ± 4 26 ± 4 26 ± 4
   Maximum, Å 0.13 ± 0.01 0.15 ± 0.01 0.15 ± 0.02 0.15 ± 0.01
Residual dihedral angle constraint violations
   No. >2.5° 0 0 0 1 ± 0
   Maximum, ° 1.3 ± 0.4 1.9 ± 0.7 1.7 ± 0.6 2.6 ± 0.4
amber energies, kcal/mol
   Total –4,821 ± 57 –4,978 ± 80 –4,879 ± 97 –4,911 ± 71
   Van der Waals –320 ± 14 –339 ± 13 –351 ± 15 –306 ± 13
   Electrostatic –5,044 ± 56 –5,598 ± 84 –5,470 ± 89 –5,523 ± 75
rms deviation to the mean coordinates, Å
   N, Cα, and C′ (125–228) 0.57 ± 0.10 0.54 ± 0.07 0.67 ± 0.08 0.60 ± 0.09
   All heavy atoms (125–228) 1.01 ± 0.09 0.95 ± 0.07 1.03 ± 0.09 1.00 ± 0.08
   N, Cα, and C′ (127–166 and 172–225) 0.53 ± 0.09 0.51 ± 0.06 0.54 ± 0.07 0.46 ± 0.06
   All heavy atoms (127–166 and 172–225) 0.96 ± 0.10 0.93 ± 0.08 0.92 ± 0.07 0.88 ± 0.06
*

Except for the top two entries, the average for the 20 conformers with the lowest residual dyana target function values and the standard deviation among them are given

The numbers in parentheses identify the polypeptide segments for which the rms deviation was calculated