Experiment: 6EYM

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

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZSJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	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 drops that was first equilibrated for 1 week. A 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. For details see Manzoni et al. (2016).
2	VAPOR DIFFUSION	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 drops that was first equilibrated for 1 week. A 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. For details see Manzoni et al. (2016).

Crystal Properties
Matthews coefficient	Solvent content
2.19	44
2.19	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.01	α = 90
b = 58.36	β = 90
c = 63.82	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	CCD	MARMOSAIC 325 mm CCD	FOCUSING MIRRORS	2015-05-31	M	SINGLE WAVELENGTH
2	1	neutron	298	IMAGE PLATE	LADI III		2014-12-15	L	LAUE
3	1	neutron	298	AREA DETECTOR	ORNL ANGER CAMERA		2015-05-15	L	LAUE

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	ILL BEAMLINE LADI III	3.35-4.35	ILL	LADI III
3	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI

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	1.07	40	99.4	0.032				1		24.7	6.6		61354
2	1.7	28	95.8	0.209			0.052			22.2	13		15485
2	1.7	28	87.1	0.162			0.044			12.4	10		13741
3	1.6	19	81.3	0.155			0.066			12.2	4.4		15485

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	1.07	1.1		0.817				0.772		2.1
2	1.7	1.8		0.334			0.139			3.9	4.9
2	1.7	1.8		0.208			0.076			7	4.9
3	1.6	1.66		0.207			0.15			2.4	1.7

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
NEUTRON DIFFRACTION	FOURIER SYNTHESIS	1.7	28				15194	769	96.2		0.17	0.168		0.211
X-RAY DIFFRACTION	FOURIER SYNTHESIS	1.1	32				56662	2815	99.4			0.107	0.117	0.125	0.1382	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	13.887
f_angle_d	1.735
f_chiral_restr	0.117
f_bond_d	0.011
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1104
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	23

Software

Software
Software Name	Purpose
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling
SCALA	data scaling
Mantid	data reduction
XPREP	data scaling
PHENIX	phasing