Table 1. Summary of MR results by MR-REX and Phaser on 38 test proteins with decoy models generated by 3DRobot and LOMETS .
For each protein multiple decoy models are attempted, where the decoy with the lowest TM-score (for the 3DRobot decoys) or with the lowest sequence identity (for the LOMETS templates) which is successfully placed with a cRMSD of <2 Å is reported in the last four columns. The data in parentheses are obtained when a successful case is defined based on phenix.autobuild, i.e. an R free of <0.4 and the model quality is improved. M and CC in the fold class column indicate membrane and coiled coil, respectively.
| Worst TM-score | Worst sequence identity (%) | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Protein PDB code | Length (amino acids) | Resolution (Å) | Solvent content | Fold class | Space group | Phaser | MR-REX | Phaser | MR-REX |
| 1d2n | 246 | 1.75 | 52 | α/β | P6 | 0.83 (0.83) | 0.82 (0.86) | 70 (70) | 27 (70) |
| 1okc | 292 | 2.20 | 55 | M | P21212 | 0.76 (0.89) | 0.76 (0.90) | 52 (52) | 52 (52) |
| 1r0u | 142 | 1.75 | 55 | β | P3221 | 0.84 (0.84) | 0.84 (0.84) | 100 (100) | 100 (100) |
| 1su0 | 136 | 2.30 | 42 | α+β | I422 | 0.79 (0.87) | 0.76 (0.83) | 22 (22) | 22 (46) |
| 1v05 | 96 | 1.43 | 35 | β | P6122 | 0.77 (0.77) | 0.77 (0.83) | 31 (31) | 31 (31) |
| 1vpq | 260 | 2.20 | 44 | α/β | C2221 | 0.82 (0.87) | 0.80 (0.91) | 33 (100) | 33 (33) |
| 1x8y | 74 | 2.20 | 71 | CC | P6522 | 0.81 (0.59) | 0.77 (0.59) | 64 (64) | 64 (64) |
| 2bou | 137 | 1.90 | 61 | β | P21212 | 0.76 (0.86) | 0.87 (0.87) | 99 (99) | 99 (99) |
| 2il5 | 162 | 2.30 | 61 | α+β | P62 | 0.74 (0.85) | 0.67 (0.85) | 12 (17) | 12 (17) |
| 2p17 | 249 | 1.52 | 32 | β | P212121 | 0.77 (0.88) | 0.79 (0.88) | 35 (35) | 35 (35) |
| 2rbk | 261 | 1.00 | 46 | α/β | P212121 | 0.79 (0.91) | 0.90 (0.90) | 21 (30) | 30 (100) |
| 2yq9 | 213 | 1.90 | 43 | α/β | P212121 | 0.74 (0.84) | 0.77 (0.82) | 48 (79) | 48 (79) |
| 3b7c | 121 | 1.70 | 56 | α+β | P6522 | 0.83 (0.84) | 0.75 (0.83) | 15 (15) | 15 (15) |
| 3bw6 | 137 | 2.50 | 66 | α/β | P3221 | 0.79 (0.79) | 0.72 (0.72) | 40 (40) | 40 (40) |
| 3chv | 279 | 1.45 | 40 | α/β | C121 | 0.74 (0.86) | 0.77 (0.93) | 61 (97) | 24 (14) |
| 3fzx | 212 | 2.20 | 59 | β | P6422 | 0.83 (0.83) | 0.81 (0.87) | 41 (41) | 41 (40) |
| 3hyn | 186 | 1.20 | 34 | α/β | P212121 | 0.86 (0.88) | 0.81 (0.83) | 96 (96) | 96 (96) |
| 3k93 | 223 | 2.15 | 60 | α/β | P321 | 0.74 (0.79) | 0.74 (0.81) | 98 (98) | 98 (98) |
| 3mt0 | 281 | 1.58 | 40 | α/β | P1211 | 0.81 (0.81) | 0.84 (0.84) | 30 (44) | 44 (44) |
| 3n2q | 282 | 2.55 | 55 | α/β | P3121 | 0.85 (0.91) | 0.86 (0.91) | 40 (40) | 40 (40) |
| 3onj | 97 | 1.92 | 35 | α | P212121 | 0.80 (0.83) | 0.74 (0.88) | 100 (100) | 100 (100) |
| 3pu6 | 138 | 2.60 | 44 | α/β | P212121 | 0.76 (0.88) | 0.68 (0.84) | 98 (98) | 98 (98) |
| 3pyw | 178 | 1.80 | 65 | α | P41212 | 0.70 (0.70) | 0.72 (0.72) | 100 (100) | 100 (100) |
| 3q6b | 155 | 1.50 | 39 | α/β | C121 | 0.62 (0.59) | 0.62 (0.59) | 18 (18) | 18 (18) |
| 3vqf | 85 | 1.20 | 43 | α/β | C121 | 0.70 (0.70) | 0.68 (0.77) | 27 (27) | 22 (22) |
| 3vwc | 146 | 1.50 | 50 | β | C121 | 0.76 (0.76) | 0.65 (0.80) | 22 (22) | 12 (22) |
| 3zdb | 246 | 1.47 | 59 | α/β | P21212 | 0.79 (0.79) | 0.76 (0.81) | 34 (34) | 34 (34) |
| 4a3z | 136 | 1.55 | 45 | β | P43212 | 0.80 (0.80) | 0.79 (0.80) | 98 (98) | 22 (98) |
| 4dcd | 184 | 1.69 | 43 | β | I222 | 0.78 (0.85) | 0.71 (0.85) | 44 (44) | 44 (44) |
| 4is7 | 140 | 2.75 | 70 | α | P6522 | 0.80 (0.80) | 0.78 (0.81) | 59 (59) | 18 (59) |
| 4kr1 | 219 | 2.50 | 52 | α/β | P6322 | 0.80 (0.80) | 0.73 (0.82) | 40 (40) | 40 (54) |
| 4l8g | 157 | 1.52 | 38 | α/β | P636 | 0.75 (0.81) | 0.75 (0.81) | 25 (37) | 25 (37) |
| 4lvp | 124 | 2.32 | 55 | α | P6422 | 0.77 (0.88) | 0.69 (0.82) | 100 (100) | 100 (100) |
| 4m6t | 177 | 2.50 | 74 | α+β | H32 | 0.70 (0.81) | 0.74 (0.74) | 100 (100) | 100 (100) |
| 4mdn | 94 | 1.91 | 68 | β | P41212 | 0.64 (0.64) | 0.65 (0.64) | 67 (67) | 67 (67) |
| 4mjf | 225 | 1.99 | 50 | α | C121 | 0.79 (0.86) | 0.74 (0.88) | 52 (97) | 52 (97) |
| 4nbr | 268 | 1.35 | 41 | α/β | I222 | 0.88 (0.88) | 0.84 (0.91) | 22 (22) | 22 (22) |
| 4oq4 | 186 | 1.49 | 59 | α/β | P3121 | 0.80 (0.80) | 0.79 (0.84) | 22 (22) | 22 (24) |
| Average | 183 | 1.88 | 60 | 0.77 (0.82) | 0.76 (0.81) | 54 (59) | 49 (58) | ||