Table 1 Refinement statistics for the three ZnuD-crystal structure intermediates solved in this study.
From: The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD
ZnuD | Cadmium (0.7 μM) co-crystallized ZnuD | Zinc-soaked (20 μM) ZnuD | |
|---|---|---|---|
PDB code | 4RDT | 4RDR | 4RVW |
Phasing method | MR | SIRAS | MR |
Data collection* | |||
Space group | P21212 | I222 | I222 |
Cell dimensions | |||
a, b, c (Å) | 101.3, 156.2, 158.0 | 101.0, 155.8, 159.6 | 101.5, 149.6, 157.6 |
α, β, γ (°) | 90, 108.5, 90 | 90, 90, 90 | 90, 90, 90 |
Wavelength (Å) | 0.9793 | 0.9793 | 1.269 |
Resolution (Å) | 49.9–3.20 (3.31–3.20) | 40.0–2.47 (2.56–2.47) | 49.6–4.47 (4.64–4.47) |
I/σI | 14.1 (3.6) | 13.4 (2.4) | 9.0 (2.9) |
Completeness (%) | 99.9 (99.8) | 99.9 (99.5) | 99.8 (99.7) |
Redundancy | 8.1 (8.0) | 15.0 (15.2) | 12.9 (13.4) |
R sym | 0.12 (0.57) | 0.14 (1.75) | 0.25 (1.76) |
CC1/2 | 0.99 (0.93) | 0.99 (0.83) | 0.99 (0.99) |
Refinement* | |||
Resolution (Å) | 49.9–3.20 | 40.0–2.47 | 49.6–4.4 |
No. of reflections | 42,108 (4,130) | 45,376 (4,479) | 7,512 (737) |
Rwork/Rfree | 0.27/0.30 | 0.21/0.24 | 0.31/0.37 |
No. of atoms | 10,159 | 5,985 | 4,839 |
Protein | 10,076 | 5,633 | 4,831 |
Ligands | 72 | 257 | 8 |
Waters | 11 | 95 | 0 |
B-factors | |||
Protein | 123.4 | 90.5 | 253 |
Ligands | 116.8 | 115.9 | 290 |
Waters | 66.1 | 91.3 | |
R.m.s deviations | |||
Bond lengths (Å) | 0.008 | 0.008 | 0.004 |
Bond angles (°) | 1.57 | 1.20 | 0.74 |
Ramachandran | |||
Favored (%) | 91.6 | 93.0 | 92.3 |
Outlier (%) | 0.3 | 0.1 | 0.3 |
