9VIS

Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU from Akkermansia muciniphila in complex with AdoCbi-GDP

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NFPSS BEAMLINE BL19U1
Synchrotron site	NFPSS
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-03-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9795
Spacegroup name	P 2 3
Unit cell lengths	89.729, 89.729, 89.729
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.860 - 1.850
R-factor	0.1804
Rwork	0.179
R-free	0.21060
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	1.078
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.920
High resolution limit [Å]	1.850	3.990	1.850
Rmerge	0.098	0.035	1.687
Rmeas	0.099	0.036	1.708
Rpim	0.016	0.006	0.270
Number of reflections	20790	2189	2060
<I/σ(I)>	4.9
Completeness [%]	100.0	100	100
Redundancy	39.3	37.3	39.9
CC(1/2)	0.999	1.000	0.834

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M Ammonium acetate 20% Polyethylene glycol 3,350