TABLE 1.
Data collection, phasing, and refinement statistics for MvNei1
Rmerge = Σ|I − 〈I〉|/ΣI, where 〈I〉 is the average intensity from multiple observations of symmetry-related reflections. Phasing power = ΣhklFH/Σ|FPH − FPH, calc|. Rwork and Rfree = Σ‖Fo| − |Fc‖/Σ|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively. Rfree was calculated with 10% of the reflections not used in refinement. MIR, multiple isomorphous replacement.
| Form-I |
Form-II |
Form-III |
||||
|---|---|---|---|---|---|---|
| Native | Iodide | Lead | Platinum | Native | MvNei1·THF complex | |
| X-rays | Home source | Home source | NSLS X29 | |||
| Space group | P65 | P1 | P21 | |||
| Unit-cell parameters (Å, °) | a = b = 123.24, c = 44.85 | a = 38.67, b = 54.42, c = 87.31 | a = 39.51, b = 121.46, c = 80.51 | |||
| α = β = 90, γ = 120 | α = 107.00, β = 99.86, γ = 93.42 | β = 95.54 | ||||
| Molecules per asymmetric unit | 1 | 2 | 2 | |||
| Data collection statistics | ||||||
| Resolution (Å) | 15-2.60 (2.69-2.60) | 15-2.70 (2.70-2.60) | 15-2.70 (2.70-2.60) | 15-3.20 (2.70-2.60) | 15-2.30 (2.42-2.30) | 35-2.2 (2.32-2.20) |
| Unique reflections | 12,173 (1,209) | 10,804 (1,085) | 10,703 (1,048) | 6,513 (654) | 27,932 (4,034) | 38,069 (5461) |
| Redundancy | 11.8 | 11.0 | 11.1 | 5.4 | 2.0 | 3.9 |
| Rmergea | 0.059 (0.270) | 0.088 (0.436) | 0.066 (0.406) | 0.183 (0.557) | 0.043 (0.146) | 0.080 (0.652) |
| Completenessa (%) | 100 (100) | 100 (100) | 98.5 (95.5) | 99.5 (100) | 94.4 (93.2) | 99.4 (97.9) |
| Overall I/σ(I)a | 44.4 (4.8) | 30.8 (5.0) | 45.0 (5.9) | 9.72 (2.22) | 17.1 (8.1) | 14.6 (2.2) |
| MIR phasing statistics | ||||||
| No. of sites | 2 | 1 | 1 | |||
| Figure of merit (solve) | 0.359 | |||||
| Figure of merit (resolve) | 0.619 | |||||
| Refinement statistics | ||||||
| Rwork (%) | 20.9 | 20.3 | 21.3 | |||
| Rfree (%) | 26.8 | 26.5 | 26.0 | |||
| r.m.s.d. values | ||||||
| Bond length (Å) | 0.0071 | 0.0057 | 0.0058 | |||
| Bond angles (°) | 1.33 | 1.22 | 1.24 | |||
| B-factor (Å2) | ||||||
| Protein | 55 | 27 | 28 | |||
| Water | 53 | 29 | 36 | |||
| DNA | 43 | |||||
| Ramachandran plot | ||||||
| Most favored (%) | 85.7 | 86.6 | 87.9 | |||
| Additional allowed (%) | 14.3 | 13.4 | 12.1 | |||
| Generously allowed (%) | 0.0 | 0.0 | 0.0 | |||
| Disallowed (%) | 0.0 | 0.0 | 0.0 | |||
| r.m.s.d. versus native (Form-I) (Å) | 0.6 (A)/0.8 (B) | 0.7 (A)/0.8 (B) | ||||
a Values for the highest resolution shell are shown in parentheses.