Table 1. Structural Statistics Reported from the Application of the RosettaOligomers Pipeline on Ten Oligomers with Experimentally Determined Structures.
| target name | PDB ID/method | size | fold/interface | data useda | Rosetta rmsd (Å)b | RDC Q-factorc |
|---|---|---|---|---|---|---|
| TolR | 2JWK/NMR | 74 × 2 | αβ/αβ | CS, RDC(1,261), SAXSd | 1.2/1.5/0.6 | 0.4 |
| ykuJ | 2FFG/X-ray | 80 × 2 | αβ/α | CS, RDC(2,59) | 0.7/0.9/0.4 | 0.26/0.18 |
| SeR13 | 2K1H/NMRe | 86 × 2 | αβ/β | CS, RDC(2,53), NOE (32) | 2.0/3.4/3.4 | 0.26/0.24 |
| At5g22580 | 1RJJ/NMR | 101 × 2 | αβ/β | CS, RDC(1,96) | 2.2/2.2/1.7 | 0.4 |
| HIV-I CCD | 1BIS/X-ray | 152 × 2 | αβ/αβ | CS, RDC(2,96) | 1.0/1.3/0.7 | 0.30/0.32 |
| yiiF | 2K5J/NMR | 44 × 2 | αβ/αβf | CS, RDC(1,24) | 0.9/1.0/0.5 | 0.05 |
| KR150 | 3OBH/X-raye | 74 × 2 | αβ/αβf | CS, RDC(1,56), NOE (67) | 1.4/2.8/2.7 | 0.32 |
| ATU0232 | 2K7I/NMR | 64 × 2 | αβ/αβf | CS, RDC(1,46) | 2.2/2.5/2.1 | 0.24 |
| CA dimer | 2KOD/NMR | 77 × 2 | α/α | CS, RDC(1,100) | 1.3/1.4/1.2 | 0.1 |
| P53 | 1C26/X-ray | 31 × 4 | αβ/αβf | CS only | 0.7/1.1/0.3 | N/A |
RDC (number of alignment media, number of RDCs per medium per monomer). All NOEs are assumed to be intramolecular. Typical estimated RDC errors are 0.5−1 Hz.
The rmsd calculated here for backbone atoms in the monomer/dimer/interface (defined here according to a 3.5 Å distance cutoff).
Q-factors calculated according to Cornilescu and co-workers(52) for alignment Media A/B (if available).
When using SAXS data in addition to RDCs, the dimer structure can be determined using a limited data set of 68 NH RDCs.
Indicating comparison to a low-resolution structural model or structure of a homologous protein.
Indicating a dimer with an interleaved interface.