6EXY

Neutron crystal structure of perdeuterated galectin-3C in complex with glycerol

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NaSCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drop that was first equilibrated for 1 week. A small crystal grown at 20-28% PEG was introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. Then the lactose was exchanged for glycerol by dialysis for at least one month against 10% glycerol (1.37 M), 24% PEG 4000 in the same buffer. For details see Manzoni et al. (2016).

Crystal Properties
Matthews coefficient	Solvent content
2.19	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.314	α = 90
b = 58.352	β = 90
c = 63.867	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	CCD	MARMOSAIC 225 mm CCD		2016-05-15	M	SINGLE WAVELENGTH
2	1	neutron	298	IMAGE PLATE	BIODIFF		2015-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3
2	NUCLEAR REACTOR	FRM II BEAMLINE BIODIFF	2.67	FRM II	BIODIFF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.1	43.1	95	0.068			0.02	1		20.2	12.3		54414			11.45
2	1.65	28.2	94.7	0.135			0.087			5.9	3.1		16592			11.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.12		1.259			0.543	0.726		1.4	7
2	1.65	1.71		0.499						1.6	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	1.1	31.93		1.34		54347	2751	94.79		0.1239	0.1231	0.1373		15.31
NEUTRON DIFFRACTION	FOURIER SYNTHESIS	1.7	28.2				15178	782	95.3		0.1522	0.1502	0.1873

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	17.6582
f_angle_d	1.7351
f_chiral_restr	0.1292
f_bond_d	0.0097
f_plane_restr	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing