21DG

Crystal structure of poly-gamma-glutamate hydrolase from Bacillus phage PM1 in complex with a zinc ion

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL45XU
Synchrotron site	SPring-8
Beamline	BL45XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-11-12
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1.000
Spacegroup name	P 42 2 2
Unit cell lengths	70.210, 70.210, 123.280
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.650 - 1.380
R-factor	0.1541
Rwork	0.153
R-free	0.17920
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.015
RMSD bond angle	1.358
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX (1.20.1_4487)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.650	1.430
High resolution limit [Å]	1.380	1.380
Rmeas	0.140	1.130
Number of reflections	64079	9769
<I/σ(I)>	7.81	1.4
Completeness [%]	99.9	99.6
Redundancy	8.1
CC(1/2)	0.990	0.692

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000, 0.5 mM zinc acetate