7Y4O

Rat Semaphorin 6D extracellular region

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-17A
Synchrotron site	Photon Factory
Beamline	BL-17A
Temperature [K]	100
Detector technology	CCD
Collection date	2012-12-19
Detector	ADSC QUANTUM 270
Wavelength(s)	0.9800
Spacegroup name	I 41
Unit cell lengths	213.147, 213.147, 191.416
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.660 - 3.000
R-factor	0.2631
Rwork	0.224
R-free	0.24430
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3afc
RMSD bond length	0.002
RMSD bond angle	0.549
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0238)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.660	3.060
High resolution limit [Å]	3.000	3.000
Rmerge	0.151	0.693
Number of reflections	169234	4516
<I/σ(I)>	7.6
Completeness [%]	99.2
Redundancy	5.1
CC(1/2)	0.985	0.710

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	12%(wt./vol.) PEG3350, 100 mM CaCl2, 400 mM sodium formate and 100 mM sodium acetate buffer (pH 4.5)