TABLE 1.
Data collection and refinement statistics
PDB, Protein Data Bank; r.m.s., root mean square.
| Structure | AKR1D1·NADP+·testosterone complex | AKR1D1·NADP+·cortisone complex | AKR1D1·NADP+·progesterone complex | AKR1D1·NADP+·HEPES complex | AKR1D1·NADP+ complex |
|---|---|---|---|---|---|
| Data collection | |||||
| PDB code | 3BUR | 3CMF | 3COT | 3BUV | 3BV7 |
| Resolution range (Å) | 50.0-1.62 | 50.0-1.90 | 30.0-2.03 | 50.0-1.35 | 50.0-1.79 |
| Unique reflections measured | 86,037 (7,952) | 51,994 (4,640) | 44,101 (4,301) | 147,700 (13,665) | 66,774 (6,684) |
| Rmergea | 0.103 (0.36)b | 0.112 (0.50)b | 0.131 (0.58)b | 0.094 (0.41)b | 0.109 (0.39)b |
| I/σ(I) | 20.3 (2.7)b | 10.9 (2.5)b | 12.2 (2.0)b | 22.6 (1.9)b | 20.5 (3.4)b |
|
Completeness (%)
|
96.0
(90.0)b |
93.7
(84.9)b |
97.6
(96.9)b |
95.7
(89.6)b |
98.6
(100.0)b |
| Refinement statistics | |||||
| Reflections used in refinement (test set) | 81,663/4,306 | 49,006/2,451 | 41,289/1,866 | 140,579/7,075 | 63,520/2,800 |
| R/Rfreec | 0.228/0.248 | 0.195/0.223 | 0.194/0.234 | 0.218/0.232 | 0.236/0.257 |
| Protein atomsd | 5,254 | 5,254 | 5,254 | 5,254 | 5,254 |
| Water moleculesd | 498 | 616 | 497 | 556 | 304 |
| NADP+ moleculesd | 2 | 2 | 2 | 2 | 2 |
| Glycerol moleculesd | 10 | 2 | 3 | ||
| Testosterone moleculesd | 2 | ||||
| Cortisone moleculesd | 2 | ||||
| Progesterone moleculesd | 2 | ||||
| HEPES moleculesd | 1 | ||||
| r.m.s. deviations | |||||
| Bond lengths (Å) | 0.007 | 0.006 | 0.007 | 0.005 | 0.012 |
| Bond angles | 1.1° | 1.2° | 1.1° | 1.2° | 1.1° |
| Average B-factors (Å2) | |||||
| Main chain atoms | 17 | 15 | 26 | 16 | 20 |
| Side chain atoms | 22 | 17 | 28 | 19 | 25 |
| Water molecules | 31 | 27 | 35 | 26 | 25 |
| NADP+ | 14 | 10 | 20 | 12 | 16 |
| Testosterone | 34 | ||||
| Cortisone | 41 | ||||
| Progesterone | 54 | ||||
| HEPES | 34 | ||||
| Glycerol | 42 | 43 | 41 | ||
| Ramachandran statisticse | |||||
| Allowed (%) | 90.4 | 89.2 | 89.0 | 89.9 | 91.1 |
| Additionally allowed (%) | 9.3 | 10.5 | 10.7 | 9.8 | 8.6 |
| Generously allowed (%) | 0.0 | 0.3 | 0.3 | 0.2 | 0.2 |
| Disallowed (%) | 0.2 | 0.0 | 0.0 | 0.2 | 0.2 |
a
Rmerge = ∑|I - <I>|/∑I, where I is the observed intensity and <I> is the average intensity calculated for replicate data.
b
The number in parentheses refer to the outer 0.1-Å shell of data.
c
Crystallographic R-factor, R = ∑(|Fo| - |Fc|)/∑|Fo| for reflections contained in the working set. Free R-factor, Rfree = ∑(|Fo| - |Fc|)/∑|Fo| for reflections contained in the test set excluded from refinement. |Fo| and |Fc| are the observed and calculated structure factor amplitudes, respectively.
d
Per asymmetric unit.
e
Ramachandran statistics were calculated with PROCHECK (29).