Experiment: 6F2Q

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

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EYM

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1351	0.1541	0.1481
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

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