6TRV

Structure of SapL1 lectin in complex with alpha methyl fucoside

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	1.5 M ammonium sulfate (NH4)2SO4 100 mM BICINE pH 8.5 12% Glycerol 10% Glycerol were added for cryoprotection

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.064	α = 90
b = 45.664	β = 105.054
c = 83.485	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 EIGER2 X 9M		2019-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.97857	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim 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	2.4	39.99	98.2	0.085	0.118	0.082	0.991	5.3	2.7		21570

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	98.4		0.428	0.598	0.417	0.7	1.6	2.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4D4U	2.4	39.99	21561	1089	97.884	0.178	0.175	0.2398	33.358

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]
-0.193		1.865	-0.899		0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.615
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	14.251
r_dihedral_angle_1_deg	8.409
r_lrange_it	6.935
r_lrange_other	6.934
r_scangle_other	5.678
r_scangle_it	5.674
r_mcangle_other	5.301
r_mcangle_it	5.298
r_scbond_it	4.183
r_scbond_other	4.175
r_mcbond_it	3.873
r_mcbond_other	3.866
r_angle_refined_deg	1.938
r_angle_other_deg	1.421
r_symmetry_nbd_other	0.209
r_nbd_refined	0.195
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.159
r_nbd_other	0.154
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.087
r_symmetry_nbd_refined	0.055
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4442
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	155

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing