9Z5T

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-06-05
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.97860
Spacegroup name	P 21 21 21
Unit cell lengths	49.865, 60.151, 111.023
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	40.830 - 2.100
R-factor	0.193
Rwork	0.191
R-free	0.23600
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.011
RMSD bond angle	1.738
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0430)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.180
High resolution limit [Å]	2.100	4.520	2.100
Rmerge	0.181	0.094	0.401
Rmeas	0.199	0.104	0.444
Rpim	0.082	0.044	0.187
Total number of observations	118798
Number of reflections	20048	2166	1985
<I/σ(I)>	8.3
Completeness [%]	99.4	99.4	99.7
Redundancy	5.9	5.9	5.6
CC(1/2)	0.929	0.894	0.885

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	9.3	291	40% PEG 600, 0.1 M CHES