Extended Data Table 1.
Crystallographic data collection and refinement statistics.
| AdoCbl-bound CarH form 1 Native * | AdoCbl-bound CarH form 1 Co Peak† | AdoCbl-bound CarH form 2 | AdoCbl-bound CarH form 3 | AdoCbl- and DNA-bound CarH | AdoCbl- and DNA-bound CarH (iodine-labeled) *† | light-exposed CarH | |
|---|---|---|---|---|---|---|---|
|
| |||||||
| PDB code | 5C8A | 5C8D | 5C8E | 5C8F | |||
| Data collection | |||||||
| Space group | P43212 | P43212 | P212121 | P1 | P21212 | P21212 | I4122 |
| Cell dimensions | |||||||
| a, b, c (Å) | 94.5, 94.5, 180.5 | 94.5, 94.5, 180.6 | 51.4, 99.7, 144.0 | 78.7, 79.7, 118.4 | 177.9, 141.8, 162.7 | 176.7, 141.7, 162.6 | 126.9, 126.9, 149.5 |
| α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.7, 96.6, 117.3 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Wavelength | 0.9792 | 1.6039 | 0.9795 | 0.9795 | 0.9795 | 1.7365 | 0.9791 |
| Resolution (Å) | 200–2.80 (2.87–2.80) | 200–3.30 (3.36–3.30) | 100–2.15 (2.21 –2.15) | 100–2.80 (2.87–2.80) | 100–3.89 (3.99–3.89) | 100–5.00 (5.13–5.00) | 100–2.65 (2.72–2.65) |
| Rsym (%) ‡ | 6.5 (69.0) | 12.4 (38.6) | 5.3 (60.8) | 10.5 (83.2) | 9.8 (126.4) | 7.2 (107.1) | 6.9 (167.8) |
| Rmeas (%) ‡ | 7.2 (76.5) | – § | 6.2 (71.5) | 11.7 (91.9) | 10.2 (131.9) | 8.6 (127.2) | 7.2 (174.4) |
| CCl/2‡ | 99.9 (77.1) | – § | 99.9 (87.7) | 99.7 (84.3) | 99.9 (87.0) | 99.9 (54.3) | 100.0 (68.5) |
| <I/σ(I)> ‡ | 16.4 (2.3) | 15.7 (7.0) | 15.2 (2.1) | 12.0 (2.0) | 15.7 (2.0) | 7.4 (1.1) | 26.8 (1.8) |
| Completeness (%)‡ | 99.5 (99.9) | 99.5 (100.0) | 98.5 (99.4) | 94.9 (95.5) | 99.9 (100.0) | 97.7 (98.2) | 100.0 (99.9) |
| Redundancy‡ | 5.3 (5.4) | 11.9 (11.5) | 3.6 (3.6) | 5.6 (5.6) | 12.2 (12.4) | 3.5 (3.3) | 12.8 (13.4) |
| Refinement | |||||||
| Resolution (Å) ‡ | 100–2.15 (2.21–2.15) | 100–2.80 (2.87–2.80) | 100–3.89 (3.99–3.89) | 100–2.65 (2.72–2.65) | |||
| No. reflections‡ | 40511 (2970) | 59284 (4419) | 38480 (2819) | 18067 (1319) | |||
| Rwork/Rfree | 0.183/0.227 | 0.183/0.230 | 0.250/0.257 | 0.172/0.203 | |||
| No. atoms | |||||||
| protein | 5766 | 14668 | 14500 | 2090 | |||
| Cbl | 364 | 728 | 728 | 91 | |||
| 5′-deoxyadenosine | 72 | 144 | 144 | – | |||
| water | 259 | – | – | 19 | |||
| DNA | – | – | 2120 | – | |||
| glycerol | 6 | – | – | 6 | |||
| chloride | – | – | – | 2 | |||
| B-factors | |||||||
| protein | 48.5 | 76.4 | 164.4 | 85.9 | |||
| Cbl | 45.1 | 65.2 | 153.9 | 100.8 | |||
| 5′-deoxyadenosine | 46.1 | 75.8 | 158.5 | – | |||
| water | 47.3 | – | – | 71.2 | |||
| DNA | – | – | 231.3 | – | |||
| glycerol | 54.3 | – | – | 95.3 | |||
| chloride | – | – | – | 94.7 | |||
| R.m.s deviations | |||||||
| Bond lengths (Å) | 0.004 | 0.005 | 0.005 | 0.004 | |||
| Bond angles (°) | 0.82 | 0.92 | 0.79 | 0.74 | |||
| Rotamer outliers (%) | 5 (0.9%) | 8 (0.6%) | 10(0.8%) | 0 (0.0%) | |||
*
Structure was not refined to completion. Oligomerization was probed by size exclusion chromatography and DNA binding by gel shift analysis.
†
Bijvoet pairs were not merged during data processing. Y30A, H42A: weakened binding at 100 nM protein.
‡
Values in parentheses indicate highest resolution bin. G160Q, G192Q: dimer, no tetramer.
§
Values were not reported in the version of Scalepack used for scaling. G160Q, G192Q: binds with reduced affinity and cooperativity and as a higher mobility (smaller size) complex.