Table 2. List of register errors spanning 100 residues or more that were found using conkit-validate in the checkMySequence benchmark data set.
Structures listed under ‘Original Structure’ correspond to structures where an error was found using conkit-validate and those listed under ‘Alternative Structure’ correspond to a PDB deposition for the same protein where the register matches that found to achieve the CMO. The residue range and size of the register error might differ due to the presence of missing residues. FSC refers to the Fourier shell correlation between the specified range of residues and the density map. For each pair of structures, calculation of the FSC was performed using the map of the original deposited model where the error was predicted. In the case of the deposited models with the alternative sequence register, the model was superimposed on the original structure using GESAMT with default parameters before calculating the FSC. Sequence identity was calculated using all residues in both chains. The ‘Passes filtering’ column refers to whether the predicted sequence-register error meets the criteria described in Section 2.6 and provides a reason why these filters might not have been passed. Suspected false positives have been marked in the last column.
| Original Structure | Alternative Structure | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDB code, chain ID | Resolution (Å) | Year | Residues | Size | FSC | Citation | Passes filtering | Suspected false positive | PDB code | Resolution (Å) | Year | Sequence identity (%) | Residues | FSC | Citation |
| 5nd8, G | 3.7 | 2017 | 44–169 | 125 | 0.33 | Khusainov et al. (2017 ▸) | Yes | No | 6s0z, F | 2.3 | 2019 | 100 | 44–169 | 0.45 | Halfon et al. (2019 ▸) |
| 5nd8, O | 3.7 | 2017 | 27–130 | 103 | 0.54 | Khusainov et al. (2017 ▸) | Yes | No | 6s0z, J | 2.3 | 2021 | 100 | 27–130 | 0.79 | Halfon et al. (2019 ▸) |
| 5xlp, D | 4.2 | 2017 | 16–339 | 323 | 0.53 | Peng et al. (2017 ▸) | Yes | No | 6vqv, E | 2.57 | 2020 | 100 | 32–357 | 0.74 | Zhang et al. (2020 ▸) |
| 5yz0, A | 4.7 | 2017 | 2–547 | 534 | 0.49 | Rao et al. (2018 ▸) | No: high Q-score | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 5yz0, A | 4.7 | 2017 | 555–1520 | 720 | 0.53 | Rao et al. (2018 ▸) | No: high Q-score | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 5yz0, A | 4.7 | 2017 | 1884–2110 | 226 | 0.61 | Rao et al. (2018 ▸) | Yes | No | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6j5i, b | 3.34 | 2019 | 3–208 | 205 | 0.34 | Gu et al. (2019 ▸) | No: insufficient contact information | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6klh, A | 3.7 | 2020 | 1861–2007 | 107 | 0.20 | Peng et al. (2020 ▸) | No: high Q-score | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6rwa, E | 4.0 | 2019 | 21–140 | 119 | 0.42 | Leidreiter et al. (2019 ▸) | Yes | No | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6uxv, F | 4.7 | 2019 | 597–779 | 168 | 0.60 | Han et al. (2020 ▸) | No: insufficient contact information | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6vyh, C | 3.0 | 2020 | 130–232 | 102 | 0.48 | Pan et al. (2020 ▸) | No: high Q-score | No | 5kvg, L | 1.7 | 2016 | 96 | 118–211 | 0.64 | Zhao et al. (2016 ▸) |
| 6w2s, 2 | 3.47 | 2020 | 644–870 | 226 | 0.43 | Neupane et al. (2020 ▸) | Yes | No | 6zp4, C | 2.9 | 2020 | 98 | 644–870 | 0.56 | Thoms et al. (2020 ▸) |
| 6xe9, A | 4.3 | 2020 | 852–1674 | 380 | 0.40 | Yang et al. (2020 ▸) | No: insufficient contact information | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6ybd, v | 3.3 | 2020 | 33–154 | 121 | 0.33 | Brito Querido et al. (2020 ▸) | No: insufficient contact information | No | 6zp4, E | 2.9 | 2020 | 98 | 33–154 | 0.09 | Thoms et al. (2020 ▸) |
| 6z6f, D | 3.11 | 2021 | 117–235 | 118 | 0.46 | Lee et al. (2021 ▸) | No: insufficient contact information | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 6zme, Lt | 3.0 | 2020 | 7–138 | 115 | 0.15 | Thoms et al. (2020 ▸) | Yes | No | 7o7y, Bt | 2.2 | 2021 | 100 | 9–138 | 0.005 | Bhatt et al. (2021 ▸) |
| 7adk, B | 2.8 | 2020 | 196–385 | 184 | 0.36 | Nottelet et al. (2021 ▸) | No: high Q-score | No | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 7kdp, A | 3.6 | 2020 | 643–768 | 125 | 0.64 | Kumar et al. (2021 ▸) | No: high Q-score | Yes | N/A | N/A | N/A | N/A | N/A | N/A | N/A |