7KF3

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2019-12-12
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 1
Unit cell lengths	59.130, 93.300, 93.770
Unit cell angles	89.06, 78.91, 87.51

Refinement procedure

Resolution	48.350 - 2.350
R-factor	0.1751
Rwork	0.174
R-free	0.21010
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5uzh
RMSD bond length	0.005
RMSD bond angle	0.747
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX (1.19.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	48.350	48.350	2.410
High resolution limit [Å]	2.350	10.510	2.350
Rmerge	0.047	0.020	0.418
Rmeas	0.064	0.028	0.562
Total number of observations	172882
Number of reflections	78643	840	5778
<I/σ(I)>	12.13	32.53	2.01
Completeness [%]	96.1	91.7	96.1
Redundancy	2.198	2.114	2.211
CC(1/2)	0.998	0.998	0.808

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	287	Microlytic Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma base pH 8.5: Braba.00085.a.AE1.PW38674 at 29.4mg/ml: tray 311690 d12: cryo: direct: puck zdr6-4.