9LAD

Crystal structure of the complex between Neuronal Pentraxin 2 (NP2 PTX) and antibody fragment VHH N1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-5A
Synchrotron site	Photon Factory
Beamline	BL-5A
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-10-27
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	1.0000
Spacegroup name	P 21 21 2
Unit cell lengths	93.574, 118.234, 39.464
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	46.800 - 2.020
Rwork	0.182
R-free	0.21970
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.618
Data reduction software	XDS (Jun 30, 2024 BUILT=20241002)
Data scaling software	Aimless (0.7.9)
Phasing software	PHASER (2.8.3)
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.800	2.070
High resolution limit [Å]	2.020	2.020
Rmerge	0.066	1.051
Rpim	0.029	0.353
Number of reflections	29010	1714
<I/σ(I)>	31.7	2.4
Completeness [%]	98.2	80.8
Redundancy	12.5	9.4
CC(1/2)	1.000	0.782

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH7.0, 12% w/v PEG 3,350.