Table 1.
Data Collection, Phasing and Refinement Statistics of the CCDC61 Crystal Structures
| Crystal | hCCDC611−143 |
zCCDC611−168;F129E/D130A |
zCCDC611−170 |
|---|---|---|---|
| SeMet (Peak) | Native | Native | |
| Beamline | DLS I02 | MRC LMB | DLS I03 |
| Wavelength (Å) | 0.9792 | 1.5418 | 0.9762 |
| Resolution (Å) | |||
| Overall | 29.68–2.55 | 44.81–1.97 | 68.31–2.90 |
| Outer shell | 2.66–2.55 | 2.02–1.97 | 3.08–2.90 |
| Space group | P22121 | P212121 | C2221 |
| Unit cell parameters | |||
| a, b, c (Å) | 36.877, 68.222, 180.728 | 55.36, 76.31, 83.24 | 93.09, 100.56, 135.76 |
| No. of unique reflections | 15,498 | 25,068 | 14,498 |
| Completeness (%) | 99.1 (99.7)a | 98.2 (96.6) | 100 (100) |
| Redundancy | 5.0 | 7.0 | 5.9 |
| Rmergeb (%) | 7.7 (56.8) | 10.2 (86.8) | 11.3 (84.9) |
| <I/σ> | 14.7 (2.3) | 12.6 (2.4) | 9.4 (2.0) |
| CC½ (%) | 99.8 (93.2) | 99.7 (75.6) | 99.9 (84.0) |
| Phasing method | Single anomalous diffraction | Molecular replacement | Molecular replacement |
| FOM | 0.339 | N/A | N/A |
| Overall score | 39.02 | N/A | N/A |
| Refinement | |||
| PDB: | 6HXT | 6HXV | 6HXY |
| Rcrystc (highest shell) (%) | 20.81 (35.02) | 17.32 (23.49) | 19.99 (29.73) |
| Rfreed (highest shell) (%) | 25.60 (41.38) | 23.79 (31.77) | 25.81 (34.88) |
| No. of atoms | |||
| Protein atoms | 2,900 | 2,559 | 2,335 |
| Water molecules | 66 | 299 | 27 |
| Average B factors (Å2) | 69.81 | 34.75 | 83.16 |
| Ramachandran plot (%) | |||
| Favoured | 97.2 | 97.8 | 96.6 |
| Outliers | 0.0 | 0.3 | 0.3 |
| Clashscore | 7.59 | 4.30 | 8.68 |
| MolProbity overall score | 1.72 | 1.25 | 1.75 |
| RMSD | |||
| Bond lengths (Å) | 0.004 | 0.008 | 0.008 |
| Bond angles (°) | 1.080 | 1.098 | 1.203 |
FOM, figure of merit; RMSD, root-mean-square deviation.
a
The statistics in parentheses are for the highest-resolution shell.
b
Rmerge = Σh|Ih − <I>|/ΣhIh, where Ih is the intensity of reflection h, and <I> is the mean intensity of all symmetry-related reflections.
c
Rcryst = Σ||Fobs| −|Fcalc||/Σ|Fobs|, Fobs and Fcalc are observed and calculated structure factor amplitudes.
d
Rfree as for Rcryst using a randomly selected 10% for hCCDC611−143 and zCCDC611−170, and 5% for zCCDC611−168;F129E/D130A of the data excluded from the refinement.