9S56

The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide

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	2024-03-06
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.9762
Spacegroup name	P 21 21 21
Unit cell lengths	45.762, 68.292, 119.041
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	59.521 - 1.668
Rwork	0.191
R-free	0.24030
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.486
Data reduction software	DIALS
Data scaling software	STARANISO
Phasing software	PHASER
Refinement software	REFMAC (5.8.0430)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	59.521	1.864
High resolution limit [Å]	1.667	1.667
Rmerge	0.320	2.442
Rmeas	0.324	2.480
Rpim	0.053	0.428
Number of reflections	30060	1511
<I/σ(I)>	9	1.7
Completeness [%]	67.8	12.2
Redundancy	37.1	33.2
CC(1/2)	0.998	0.760

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.3% Sodium-L ascorbate, 0.3% Choline Chloride, 0.3% D-Panthenol, 0.3% Pyridoxine hydrochloride, 0.3% Thiamine hydrochloride, 0.3% CHAPS, 0.3% CHAPSO, 0.3% Sodium glycocholate hydrate, 0.3% Taurocholic acid sodium salt hydrate, 100 mM Tris/Bicine, 10% PEG 20,000, 20% PEG 500 MME