9I4G

Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in complex with D-galactose

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-30
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97626
Spacegroup name	P 1 21 1
Unit cell lengths	107.011, 129.025, 108.404
Unit cell angles	90.00, 90.13, 90.00

Refinement procedure

Resolution	107.011 - 2.980
Rwork	0.227
R-free	0.26080
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	1.300
Data reduction software	XDS (BUILT 20230630)
Data scaling software	XDS (BUILT 20230630)
Phasing software	PHASER (2.8.3)
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	107.011	107.011	3.030
High resolution limit [Å]	2.978	8.084	2.978
Rmeas	0.234	0.063	0.772
Rpim	0.103	0.028	0.358
Number of reflections	60001	3023	2934
<I/σ(I)>	6.4	15.7	2.1
Completeness [%]	99.4	97.4	99.2
Redundancy	5	4.7	4.5
CC(1/2)	0.989	0.997	0.834

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.4	293	0.2 M lithium citrate, 20% PEG 3350