4JJH

Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS BEAMLINE X29A
Synchrotron site	NSLS
Beamline	X29A
Temperature [K]	100
Detector technology	CCD
Collection date	2013-02-07
Detector	ADSC QUANTUM 315
Wavelength(s)	1.0750
Spacegroup name	P 41
Unit cell lengths	35.193, 35.193, 205.331
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.193 - 2.250
R-factor	0.2257
Rwork	0.222
R-free	0.29210
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4frw
RMSD bond length	0.011
RMSD bond angle	1.488
Data reduction software	DENZO
Data scaling software	SCALEPACK
Phasing software	PHENIX (1.8.2_1309)
Refinement software	PHENIX (1.8.2_1309)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.290
High resolution limit [Å]	2.250	6.100	2.250
Rmerge	0.069	0.053	0.262
Number of reflections	11529
<I/σ(I)>	8.3
Completeness [%]	97.3	96.3	100
Redundancy	9	8.3	9.5

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K