9RFJ

Crystal structure of the metallo-beta-lactamase VIM-1 with 2492

This is a non-PDB format compatible entry.

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	2025-03-31
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.78380
Spacegroup name	P 1 21 1
Unit cell lengths	39.422, 67.859, 40.149
Unit cell angles	90.00, 93.28, 90.00

Refinement procedure

Resolution	33.930 - 1.150
R-factor	0.1286
Rwork	0.127
R-free	0.15540
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.162
Data reduction software	xia2
Data scaling software	pointless
Phasing software	PHASER
Refinement software	REFMAC (9.0.003)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	34.510	1.170
High resolution limit [Å]	1.150	1.150
Rmerge	0.088	0.836
Rmeas	0.095	0.909
Rpim	0.036	0.352
Total number of observations		24427
Number of reflections	74815	3711
<I/σ(I)>	10.3	1.8
Completeness [%]	100.0
Redundancy	6.9	6.6
CC(1/2)	0.999	0.745

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	2.6M ammonium phosphate, 0.1M tris, pH 8.5