6F2Q

Neutron crystal structure of perdeuterated galectin-3C in the ligand-free form

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 THEN INTRODUCED. THE DROP WAS FED WITH FRESH PROTEIN BY ADDING 3-4 MICROLITRES OF PROTEIN WITH 10 MM LACTOSE EVERY 3-4 DAYS FOR 3 MONTHS. LACTOSE WAS THEN REMOVED IN TWO STEPS, FIRST BY DIALYSING AGAINST 1M GLYCEROL FOR 1 MONTH THEN AGAINST BUFFER WITH NO GLYCEROL FOR 1 MONTH. FOR DETAILS, SEE MANZONI ET AL. (2016).

Crystal Properties
Matthews coefficient	Solvent content
2.19	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.39	α = 90
b = 58.62	β = 90
c = 64.02	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	ADSC QUANTUM 315r	FOCUSING MIRRORS	2017-03-10	M	SINGLE WAVELENGTH
2	1	neutron	298	IMAGE PLATE			2017-02-15	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98081	ESRF	BM30A
2	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.35-4.35	ILL	LADI III

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	1.03	28	99.8	0.044			0.012	1		35.5	14		70173
2	1.8	30	83.8		0.132		0.053	0.993		8.5	4.9		9844

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	1.03	1.06		2.357			0.933	0.355		1	9.3
2	1.8	1.9		0.194			0.091	0.917			3.4

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	1.03	29.31		1.35		70165	4369	99.82		0.1384	0.1373	0.1541
NEUTRON DIFFRACTION	FOURIER SYNTHESIS	1.757	28.094				11785	735	80.83		0.1741	0.1715	0.2107

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	16.358
f_dihedral_angle_d	16.358
f_angle_d	1.43
f_angle_d	1.43
f_chiral_restr	0.107
f_chiral_restr	0.107
f_bond_d	0.011
f_bond_d	0.011
f_plane_restr	0.009
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
LAUEGEN	data scaling
PHENIX	phasing