Table 3.
Molecule (PDB ID) | M (Da) | RT,expa (Å) | RT,calc (Å) | % Signed Error | RR,expa (Å) | RR,calc (Å) | a/bb | Reference(s) | |
---|---|---|---|---|---|---|---|---|---|
DNA duplex 8merc | 4850 | 14.1 | 13.8 | −1.9 | 14.5 | 14.8 | 1.13 | (33, 65) | |
DNA duplex 12mer (5NT5) | 7331 | 16.6d | 16.4 | −1.2 | 18.3 | 18.0 | 1.61 | (33, 35, 36) | |
DNA duplex 20mer (5F9I) | 12,288 | 19.7 | 20.5 | +4.1 | 25.0 | 24.7 | 2.62 | (33) | |
DNA duplex 24mere | 14,758 | 22.5 | 22.6 | +0.4 | ND | ND | 2.92 | (34) | |
tRNA-HisRS (4RDX) | 70,463 | 37.4 | 37.8 | +1.1 | ND | ND | 1.60 | (39) | |
Bacteria ribosome 50S (5HKV) | 1,263,178f | 92.9 | 95.32 | +2.6 | ND | ND | 1.26 | (40) | |
mean % signed error | +0.85 |
ND, not determined.
Experimental hydrodynamic coefficients as reported in the references were converted to RT or RR for comparison.
Axial ratio of prolate ellipsoid with maximum dimension and volume equal to the respective convex hull.
The structure in PDB file 5NT5 was edited to be equivalent to an 8mer.
Average of values reported in cited references.
The structure in PDB file 5F9I was used to model a 24mer with the same pitch.
Molar mass of the structure in 5HKV. A reported actual molar mass of 1,364,954 g mol−1 (107) was used with a sedimentation coefficient of 50.0 and partial specific volume of 0.614 to calculate RT,exp.