8PFE

Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex with the KDKPPR Peptide

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE BM07
Synchrotron site	ESRF
Beamline	BM07
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-10-11
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.979511
Spacegroup name	P 32 2 1
Unit cell lengths	59.773, 59.773, 174.604
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	19.570 - 1.350
R-factor	0.1949
Rwork	0.194
R-free	0.21000
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.012
RMSD bond angle	1.150
Data reduction software	XDS (VERSION Feb 5, 2021 BUILT=20210323)
Data scaling software	Aimless (version 0.7.4 : 13/12/18)
Phasing software	MOLREP
Refinement software	BUSTER (2.10.4 (21-NOV-2022))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.530	1.370
High resolution limit [Å]	1.350	1.350
Rmerge	0.031	0.681
Rmeas	0.033	0.779
Rpim	0.011	0.369
Number of reflections	80230	3895
<I/σ(I)>	28.7	1.9
Completeness [%]	99.7	95.7
Redundancy	8.7	4.2
CC(1/2)	1.000	0.685

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.3 ul protein + 0.3 ul crystallization solution (0.2 M ammonium citrate, 0.1 M bis-tris pH 5.5 and 25% w/v PEG 3350, from JCSGplus); soaked in their mother liquor supplemented with 20% glycerol