9PL6

Crystal Structure of the Peptide-binding Protein NikA from Streptococcus agalactiae in Complex with Zinc, L-Histidine, Imidazole and Ethylene Glycol.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-10-15
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	0.92020
Spacegroup name	P 1 21 1
Unit cell lengths	76.031, 58.310, 122.115
Unit cell angles	90.00, 107.33, 90.00

Refinement procedure

Resolution	29.160 - 1.950
R-factor	0.18962
Rwork	0.187
R-free	0.23918
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	1.523
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHASER
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	30.000	1.980
High resolution limit [Å]	1.950	1.950
Rmerge	0.106	0.574
Rmeas	0.131	0.721
Rpim	0.076	0.432
Number of reflections	70920	3448
<I/σ(I)>	8.7	1.6
Completeness [%]	95.4	94.1
Redundancy	2.5	2.4
CC(1/2)	0.986	0.628

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 12.9 mg/ml, 10mM HEPES (pH 7.2), 1mM TCEP, 2% Glycerol, 5mM Imidazole; Screen: Classics II (D8), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350; Cryo: Reservoir.