9F0Q

VIM-2 in complex with GKV53 (5d) - dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors

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 P14 (MX2)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P14 (MX2)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-08-19
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.8
Spacegroup name	C 1 2 1
Unit cell lengths	101.804, 79.021, 67.815
Unit cell angles	90.00, 130.76, 90.00

Refinement procedure

Resolution	55.190 - 1.920
R-factor	0.1734
Rwork	0.171
R-free	0.21330
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.889
Data reduction software	autoPROC (1.1.7)
Data scaling software	autoPROC (1.1.7)
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	55.190	1.950
High resolution limit [Å]	1.920	1.920
Rmerge	0.140	0.980
Rmeas	0.154	1.066
Rpim	0.058	0.397
Number of reflections	30937	1551
<I/σ(I)>	9.8	2.2
Completeness [%]	99.3	99.4
Redundancy	7	7.1
CC(1/2)	0.997	0.802

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	protein solution: 10.3 mg/ml in 50 mM Tris/HCl, pH 7.2, 100 uM ZnCl2 crystallization agent: 20 mM inhibitor, 25% polyethylene glycol (PEG) 3350, 0.2 M magnesium formate cryo protectant solution: (20 mM inhibitor, 25% PEG3350, 15% Ethylene glycol, 0.2 mM MgCl2, 50 mM HEPES pH 7.2)