Table 1. Data collection and refinement statistics.
Data collection was carried out at Beamline 5C at Pohang Accelerator Laboratory (PAL), Republic of Korea.
| Data collection | |||
| Dataset | EFhd1Ca | EFhd1Zn | EFhd2Zn |
| Final Ca2+ conc. (mM) | 3 | 0.5 | – |
| Final Zn2+ conc. (mM) | 0.1 | 1.3 | 0.4 |
| Space group | P212121 | P212121 | I23 |
| X-ray source | PAL-5C | PAL-5C | PAL-5C |
| Detector | EIGER 9M | EIGER 9M | EIGER 9M |
| Wavelength (Å) | 1.2826 | 1.2826 | 1.2851 |
| Unit cell parameters | |||
| a, b, c (Å) | 44.3, 47.9, 63.4 | 44.0, 47.4, 63.4 | 92.8, 92.8, 92.8 |
| α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Resolution range (Å)† | 50–2.80 (2.85–2.80) | 50–1.72 (1.75–1.72) | 50–2.60 (2.72–2.60) |
| R merge ‡ | 16.4 (49.2) | 7.9 (82.9) | 9.6 (133.9) |
| CC1/2 | 0.999 (0.959) | 0.998 (0.774) | 1.00 (0.960) |
| 〈I/σ(I)〉 | 20.0 (3.7) | 24.4 (2.1) | 40.3 (4.0) |
| Completeness (%) | 99.8 (98.3) | 99.5 (94.5) | 100.0 (100.0) |
| Redundancy§ | 22.0 (10.0) | 12.5 (9.8) | 80.8 (82.0) |
| Refinement | |||
| Resolution range (Å) | 31.7–2.80 | 38.0–1.72 | 46.5–2.60 |
| No. of unique reflections | 3614 | 14742 | 4243 |
| R work/R free (%)¶ | 19.5/25.2 | 19.8/21.1 | 22.9/26.0 |
| B factors (Å2) of protein | 38.9 | 22.3 | 67.2 |
| No. atoms (residues) | |||
| Protein | 827 (102) | 813 (102) | 775 (99) |
| Glycerol | 6 (1) | 6 (1) | 0 |
| Ca2+ | 2 | 0 | 0 |
| Zn2+ | 1 | 4 | 3 |
| Water | 20 | 32 | 5 |
| Model statistics | |||
| RMSD bond length (Å) | 0.009 | 0.009 | 0.010 |
| RMSD bond angle (°) | 1.039 | 0.984 | 1.184 |
| Ramachandran plot (%) | |||
| Favored | 99.0 | 99.0 | 95.9 |
| Allowed | 1.0 | 1.0 | 4.1 |
| Disallowed | 0.0 | 0.0 | 0.0 |
| PDB entry | 7ygv | 7ygw | 7ygy |
†
Values in parentheses are for the highest resolution shell.
‡
R merge = ∑ h ∑ i |I(h) i − 〈I(h)〉|/[∑ h ∑ i I(h) i ], where I(h) is the intensity of the reflection of h, ∑ h is the sum over all reflections and ∑ i is the sum over i measurements of reflection h.
§
Redundancy: we collected EFhd1Ca and EFhd2Zn datasets using 720 frames, and EFhd1Zn datasets using 360 frames due to the radiation decay.
¶
R work = ∑ hkl ||F o|−|F c||/(∑ hkl |F o|); 5% of the reflections were excluded for the R free calculation.