8DOQ
Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P21 Form)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 19-ID |
Synchrotron site | NSLS-II |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-04-08 |
Detector | DECTRIS EIGER2 XE 9M |
Wavelength(s) | 0.97949 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 49.350, 70.500, 66.840 |
Unit cell angles | 90.00, 90.91, 90.00 |
Refinement procedure
Resolution | 39.400 - 1.650 |
R-factor | 0.1807 |
Rwork | 0.179 |
R-free | 0.20940 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8dop |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 70.500 | 70.500 | 1.690 |
High resolution limit [Å] | 1.650 | 7.380 | 1.650 |
Rmerge | 0.094 | 0.071 | 0.355 |
Rmeas | 0.111 | 0.084 | 0.418 |
Rpim | 0.058 | 0.044 | 0.218 |
Total number of observations | 194613 | 2297 | 14531 |
Number of reflections | 55090 | 644 | 4027 |
<I/σ(I)> | 6.4 | 12.8 | 2.2 |
Completeness [%] | 99.9 | 98.3 | 99.6 |
Redundancy | 3.5 | 3.6 | 3.6 |
CC(1/2) | 0.992 | 0.986 | 0.896 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: PSL0809, Cryo: DIRECT; Electron density consistent with a benzoic acid molecule was observed and modeled. The source of this is unknown and it may have been acquired from the expression host |