Experiment: 8AD2

Tobacco lectin Nictaba in complex with triacetylchitotriose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		apo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	287	100 mM ZnAc, 100 mM ZnCl2, 100 mM Bis-Tris pH 7.5, 20 % Medium smear. Soaked and cryoprotected in ML supplemented with 5% (v/v) glycerol, 5% (v/v) ethylene glycol , 5% (v/v) DMSO, 1 mM triacetylchitotriose.

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.66	α = 90
b = 146.159	β = 95.874
c = 81.908	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2	60.39	93.4	0.132	0.996	8.01	4.06		97998			32.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12	69.2		1.109	0.51	1.23	3.62

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	apo	2	54.22	1.35	97974	2000	93.37	0.1961	0.1955	0.1958	0.2261	0.2258	38.86

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	19.3348
f_angle_d	1.2513
f_chiral_restr	0.0712
f_bond_d	0.0131
f_plane_restr	0.0084

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10688
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	196

Software

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