5LFU

Myelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full extracellular domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1URL	1URL, 4FRW, 1CS6, 3P3Y, 2YD6
experimental model	PDB	4FRW	1URL, 4FRW, 1CS6, 3P3Y, 2YD6
experimental model	PDB	1CS6	1URL, 4FRW, 1CS6, 3P3Y, 2YD6
experimental model	PDB	3P3Y	1URL, 4FRW, 1CS6, 3P3Y, 2YD6
experimental model	PDB	2YD6	1URL, 4FRW, 1CS6, 3P3Y, 2YD6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a condition containing 200 mM NaOAc and 20 % PEG3350 (w/v).

Crystal Properties
Matthews coefficient	Solvent content
7.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.237	α = 90
b = 101.237	β = 90
c = 687.477	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2013-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.97553	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	4.3	114.62	100	0.115	15.6	35.7		15430

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.3	4.81	100		3.937	1.3	36.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1URL, 4FRW, 1CS6, 3P3Y, 2YD6	4.3	114.579	1.34	15425	769	99.97	0.2859	0.2855	0.2955	Random selection

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.155
f_angle_d	1.331
f_chiral_restr	0.198
f_bond_d	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3776
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	166

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.