5LF5 | pdb_00005lf5

Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand

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	7	291	100 mM NaCl, 20 mM Tris/HCl pH 7.0, 7.7 % PEG 4000 (w/v)

Crystal Properties
Matthews coefficient	Solvent content
12.7	90.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 278.868	α = 90
b = 278.868	β = 90
c = 62.52	γ = 120

Symmetry
Space Group	P 32 2 1

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 PILATUS3 6M		2013-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99998	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	3.8	52.7	100	0.233	0.997	9.3	9.6		27623

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.8	4.03	100		1.685	0.565	1.6	9.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1URL, 4FRW, 1CS6, 3P3Y, 2YD6	3.8	52.701	1.34	27582	1407	99.89	0.2005	0.199	0.21	0.2281	0.24	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	14.034
f_angle_d	1.397
f_chiral_restr	0.192
f_plane_restr	0.013
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3750
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	137

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	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 R01GM157729.