Experiment: 5FB8

Structure of Interleukin-16 bound to the 14.1 antibody

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I7Z	1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C
experimental model	PDB	4F33	1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C
experimental model	PDB	1I16	1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	16% PEG3350, 0.1 M Bis-Tris-Propane, pH 6.5 and 0.2 M sodium sulphate.

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.69	α = 90
b = 65.95	β = 90
c = 196.44	γ = 90

Symmetry
Space Group	P 21 21 21

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		2013-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

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	2.07	29.45	99.81	0.055	17.79	6.3		48100

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	2.07	2.144	99.85		0.695	3.44	6.5

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C	2.07	29.45	1.34	48095	2434	99.8	0.1735	0.1718	0.1844	0.2053	0.2147

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	13.864
f_angle_d	1.15
f_chiral_restr	0.044
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3997
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	51

Software

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