Table I.
Crystallographic Statistics for the SipD Crystals
| apo SipD | apo SipD C244S | SipD C244S –deoxycholate | SipD-chenodeoxycholate | |
|---|---|---|---|---|
| PDB ID | 3NZZ | 3O00 | 3O01 | 3O02 |
| Data collection | ||||
| Unit-cell parameters (Å,°) | a = 203.06 | a = 203.35 | a = 201.93 | a = 202.22 |
| b = 52.25 | b = 52.15 | b = 52.33 | b = 52.37 | |
| c = 57.52 | c = 57.56 | c = 57.31 | c = 57.32 | |
| β = 90.05 | β = 90.45 | β = 90.3 | β = 90.20 | |
| Space group | C2 (No. 5) | C2 (No. 5) | C2 (No. 5) | C2 (No. 5) |
| Resolution rangea | 50.0–1.65 (1.71–1.65) | 50.0–1.85 (1.92–1.85) | 50.0–1.9 (1.97–1.90) | 50.0–1.9 (1.97 – 1.90) |
| Wavelength (Å) | 1.0000 | 1.000 | 1.000 | 1.000 |
| Temperature (K) | 100 | 100 | 100 | 100 |
| Observed reflections | 256,708 | 195,676 | 170,803 | 169,943 |
| Unique reflections | 69,282 | 50,066 | 46,924 | 46,661 |
| <I/σ(I)>a | 39.2 (1.9) | 36.1 (3.5) | 20.3 (1.9) | 27.9 (3.7) |
| Completeness | 95.5 (86.1) | 97.0 (81.6) | 98.5 (88.1) | 97.9 (83.5) |
| Redundancya | 3.7 (3.0) | 3.9 (3.3) | 3.6 (3.1) | 3.69 (2.8) |
| Rmerge (%)ab | 4.4 (49.6) | 5.3 (32.4) | 5.3 (38.1) | 5.3 (23.0) |
| Refinement | ||||
| Resolution (Å) | 25.35 – 1.65 | 32.07–1.85 | 27.98–1.90 | 24.97–1.90 |
| Reflections (working/test) | 62,042/3, 296 | 46,099/2,477 | 42,527/2,249 | 43,463 / 2,308 |
| Rfactor/Rfree (%)c | 19.7/23.7 | 19.5 / 24.6 | 19.6 / 25.8 | 18.5 / 23.6 |
| No. of atoms (protein (A:B)/Ni2+/ligand/water) | 2,190:2,018/1/348 | 2,186:2,019/1/297 | 2,184:2,053/1/28/252 | 2,177:2,032/1/28/330 |
| Model quality | ||||
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.014 | 0.015 | 0.017 | 0.018 |
| Bond angles (°) | 1.478 | 1.461 | 1.556 | 1.614 |
| Average B factor (Å2) | ||||
| All atoms | 29.6 | 29.7 | 32.0 | 28.2 |
| Protein (chain A/B) | 29.0 / 29.2 | 28.6 / 30.3 | 31.5 / 32.3 | 27.6 / 27.9 |
| Ni2+ | 22.0 | 21.3 | 26.6 | 21.8 |
| Deoxycholate or chenodeoxycholate | – | – | 28.6 | 26.2 |
| Water | 35.4 | 34.0 | 34.6 | 33.5 |
| Coordinate error based on maximum likelihood (Å) | 0.25 | 0.26 | 0.26 | 0.26 |
| Ramachandran plot | ||||
| Most favored (%) | 99.1 | 98.9 | 98.9 | 98.9 |
| Additionally allowed (%) | 0.9 | 1.1 | 1.1 | 1.1 |
a
Values in parentheses are for the highest resolution shell.
b
Rmerge = ΣhklΣi|Ii(hkl) − <I(hkl)>|/ΣhklΣi|Ii(hkl), where Ii(hkl) is the intensity measured for the ith reflection and <Ii(hkl)> is the average intensity of all reflections with indices hkl.
c
Rfactor = Σhkl||Fobs (hkl)| − |Fcalc (hkl)||/Σhkl|Fobs (hkl)|; Rfree is calculated in an identical manner using 5% of randomly selected reflections that were not included in the refinement.