6Y78

Structure of galectin-3C in complex with lactose determined by serial crystallography using a silicon nitride membrane support

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	Crystals were grown on XtalTool supports (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop was made up of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7.4, 100 mM NaCl, 10 mM beta-mercaptoethanol, 2 mM lactose, 0.25 microlitres of galectin-3C seed crystals in a stabilization solution containing 0.1 M Tris pH 7.5, 33% (w/v) PEG 4000, 0.1 M MgCl2, 0.2 M NaSCN and 0.75 microlitres reservoir solution containing 0.1 M Tris pH 7.5, 34% (w/v) PEG 4000, 0.2 M NaSCN and 8 mM beta-mercapthoethanol. Crystals grew to a size of approximately 10-15 micrometer.

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.67	α = 90
b = 56.36	β = 90
c = 61.17	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	298	PIXEL	DECTRIS EIGER X 16M		2019-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9800	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	silicon nitride membrane (Silson)	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Sample Solvent
1	silicon nitride membrane		cryo cap	MD3 (Arinax)

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1	13522		32303

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.7	61	100	0.155	5.3	195.2		14154			21.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.75	100		1.833	1.41	133.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6EYM	1.7	41.45	13586	678	96.29	0.1672	0.1656	0.197	28.49

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	13.0291
f_angle_d	1.5933
f_chiral_restr	0.0636
f_bond_d	0.0199
f_plane_restr	0.0085

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1106
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	23

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.