8DQB
Crystal structure of 3-dehydroquinate dehydratase I from Klebsiella oxytoca (I23 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 | 2022-06-07 |
Detector | DECTRIS EIGER2 XE 9M |
Wavelength(s) | 0.97856 |
Spacegroup name | I 2 3 |
Unit cell lengths | 164.124, 164.124, 164.124 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 41.030 - 2.500 |
R-factor | 0.205 |
Rwork | 0.203 |
R-free | 0.23890 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2o7p |
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] | 116.050 | 116.050 | 2.570 |
High resolution limit [Å] | 2.500 | 11.180 | 2.500 |
Rmerge | 0.089 | 0.027 | 1.158 |
Rmeas | 0.094 | 0.029 | 1.216 |
Rpim | 0.029 | 0.010 | 0.369 |
Total number of observations | 264742 | 2769 | 20245 |
Number of reflections | 25537 | 318 | 1886 |
<I/σ(I)> | 18.6 | 55.4 | 2.2 |
Completeness [%] | 100.0 | 99.4 | 100 |
Redundancy | 10.4 | 8.7 | 10.7 |
CC(1/2) | 0.999 | 0.999 | 0.744 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2,KloxA.17380.a.B1.PW39095 at 5 mg/mL with 2.5 GDP added, no electron density observed for the GDP, Tray: plate 12679, well A2 drop 3, Puck: PSL1405, Cryo: DIRECT |