8DQ9

Crystal structure of GDP bound 3-dehydroquinate dehydratase I from Klebsiella oxytoca

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 2 2
Unit cell lengths	74.342, 89.761, 223.744
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	55.940 - 2.800
R-factor	0.2329
Rwork	0.230
R-free	0.27910
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]	83.310	83.310	2.870
High resolution limit [Å]	2.800	12.520	2.800
Rmerge	0.111	0.058	0.978
Rmeas	0.120	0.065	1.055
Rpim	0.045	0.028	0.391
Total number of observations	133275	1283	9740
Number of reflections	18874	240	1363
<I/σ(I)>	11.5	25.1	2.2
Completeness [%]	99.9	96.8	100
Redundancy	7.1	5.3	7.1
CC(1/2)	0.998	0.995	0.879

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	Morpheus H8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine, KloxA.17380.a.B1.PW39095 at 5 mg/mL with 2.5 GDP added. Tray: plate 12679, well H8 drop 3, Puck: PSL1316, Cryo: DIRECT