Experiment: 5J06

Structure of the immune receptor CD33 in complex with 3'-sialyllactose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IHB	PDB ENTRY 5IHB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295.15	2% PEG 20,000, 4% PEG MME 500, 100 MM BICINE/TRIS BASE PH 8.5, 1XMORPHEUS AMINO ACIDS. CRYSTALS SOAKED IN 20 MM 3'-SIALYLLACTOSE IN MOTHER LIQUOR FOR 10 DAYS.

Crystal Properties
Matthews coefficient	Solvent content
2.93	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.05	α = 90
b = 127.06	β = 90
c = 142.83	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 PILATUS 6M		2015-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

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	2.66	62.255	100	0.0902	0.997	11.7	4.3		34631			58.87

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	2.66	2.755	100		0.919	1.48	4.4

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	THROUGHOUT	PDB ENTRY 5IHB	2.66	62.255	1.34	34627	1707	99.54	0.2106	0.2088	0.2092	0.2441	0.2435	RANDOM

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	9.822
f_angle_d	0.603
f_chiral_restr	0.046
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6673
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	251

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XSCALE	data scaling
PHASER	phasing
RESOLVE	model building