6Z2Q

Crystal structure of wild type OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (GalGalNAc-TS) product

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-11-27
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.976220
Spacegroup name	P 41 21 2
Unit cell lengths	65.366, 65.366, 187.654
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.233 - 2.347
R-factor	0.203
Rwork	0.200
R-free	0.25120
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6z2d
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	29.233	2.430
High resolution limit [Å]	2.347	2.347
Rmerge	0.134	0.960
Rmeas	0.139	1.007
Number of reflections	17627	1530
<I/σ(I)>	19.29	2.91
Completeness [%]	98.6	87.13
Redundancy	12.7	10.6
CC(1/2)	0.999	0.295

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		291	100mM sodium HEPES/MOPS pH 7.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) and 50% (w/v) of precipitant mix based on 40% (w/v) PEG 500 MME and 20% (w/v) PEG 20,000 (Morpheus protein crystallization screen).