8KD0

Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL32XU
Synchrotron site	SPring-8
Beamline	BL32XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-06-09
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.0
Spacegroup name	P 32 2 1
Unit cell lengths	43.879, 43.879, 328.555
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	38.029 - 1.675
Rwork	0.194
R-free	0.22880
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	8hqq
RMSD bond length	0.007
RMSD bond angle	1.368
Data reduction software	XDS (Jun 30, 2023)
Data scaling software	XDS (Jun 30, 2023)
Phasing software	MOLREP (11.9.02)
Refinement software	REFMAC (5.8.0405)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.936	1.780
High resolution limit [Å]	1.670	1.670
Rmerge	0.135	1.608
Rmeas	0.141	1.683
Number of reflections	43960	6771
<I/σ(I)>	11.08	1.05
Completeness [%]	99.6	97.3
Redundancy	12.2	11.37
CC(1/2)	0.997	0.864

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	6.5	293	20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant.