Table 1.
Data reduction, phasing and refinement statistics
| Type I, IB1 SH3-S, SeMet | Type II, IB1 SH3-S, SeMet | Type III, IB1 SH3-L | |
|---|---|---|---|
| Data collection | |||
| X-ray source, wavelength (Å) | BL711/MaxLab, 0.967 | X11/EMBL-Hamburg, 0.811 | ID29/ESRF, 0.979 |
| Space group | P42212 | P21212 | P212121 |
| Cell dimensions (Å) | a=b=114.5, c=48.4 | a=75.6, b=81.6, c=89.7 | a=45.9, b=57.0, c=145.5 |
| Monomer per asymmetric unit | 4 | 8 | 4 |
| Resolution range (Å) | 25–2.05 (2.16–2.05)a | 20–1.75 (1.84–1.75) | 30–3.0 (3.19–3.00) |
| Unique reflections | 37 925 (5354) | 54 422 (7198) | 8075 (782) |
| Average multiplicity | 8.0 (8.2) | 4.5 (3.7) | 4.6 (4.2) |
| Completeness (%) | 98.3 (97.4) | 96.2 (88.5) | 99.2 (100.0) |
| 〈I/σI〉 | 7.7 (2.3) | 20.8 (2.6) | 12.1 (2.9) |
| Rmergeb (%) | 9.6 (34.0) | 5.6 (32.4) | 10.2 (46.1) |
| Phasing | |||
| Heavy atom sites | 4 | ||
| Resolution range (Å) | 40–2.65 | ||
| Figure of merit (acentric/centric) | 0.34/0.11 | ||
| Phasing power (anomalous)c | 1.17 | ||
| Rcullisd (iso/ano) | 0.79 | ||
| Refinement | |||
| Rwork/Rfreee (%) | 18.4/22.8 | 20.4/23.5 | 22.4/25.1 |
| Number of atoms | |||
| Protein | 2100 | 4181 | 511 |
| Water | 249 | 597 | 0 |
| Hetero | 33 | 95 | 0 |
| Average B-factor (Å2) | |||
| Protein | 19 | 21 | 51 |
| Water | 29 | 34 | — |
| Hetero | 48 | 56 | — |
| R.m.s. deviation | |||
| Bond lengths (Å) | 0.006 | 0.005 | 0.007 |
| Angles (deg) | 1.4 | 1.4 | 1.4 |
| Ramachandran plotsf | |||
| Most favored regions (%) | 88.2 | 89.9 | 84.9 |
| Additional allowed regions (%) | 11.4 | 9.8 | 15.1 |
| aValues in parentheses refer to the highest resolution bin. | |||
| bRmerge=∑hkl(∑i(∣Ihkl, i−〈Ihkl〉∣))/∑hkl, i〈Ihkl〉, where Ihkl, i is the intensity of an individual measurement of the reflection with Miller indicies h, k and l, and 〈Ihkl〉 is the mean intensity of that reflection. | |||
| cPhasing power=∑hklFH, hkl/∑hkl∣FPH, obs, hkl−FPH, calc, hkl∣. | |||
| dRcullis=∑hkl∣∣FPH, hkl±FP, hkl∣−FH, calc, hkl∣/∑hkl∣FPH, hkl−FP, hkl∣, where FPH is the structure factor of the heavy atom derivative, FP is the structure factor of the native protein and FH, calc is the calculated structure factor for the heavy atom. | |||
| eRwork=∑hkl(∣∣Fobs, hkl∣−∣Fcalc, hkl∣∣)/∣Fobs, hkl∣, where ∣Fobs, hkl∣ and ∣Fcalc, hkl∣ are the observed and calculated structure factor amplitudes. Rfree is equivalent to the Rwork, but calculated with 5.7% (Type I), 2.1% (Type II) and 7.4% (Type III) of the reflections omitted from the refinement process. | |||
| fValues from PROCHECK (CCP4, 1994). | |||